Blue Box, Blue Bots
by The Incredible Muffin
Summary: Just when Jack and June Darby find themselves missing a certain Time Lord, he returns. Unfortunately, he returned right in the middle of the Autobot base. Can the Decepticons withstand the Oncoming Storm, and how long can the Autobots stand before the man with the blue box drives them insane?
1. It Starts with a Box

**DOCTOR WHO DOES NOT BELONG TO ME. TRANSFORMERS DOES NOT BELONG TO ME. THE WEEPING ANGELS CAN STAY WHERE THEY ARE, BECAUSE THEY SCARE THE DAYLIGHTS OUT OF ME.**

**Hello, everyone! I'm The Incredible Muffin, and have I got a story for you! I know that those of you who regularly follow me did not see this story coming, but I've had this one in my brain for a long time and **_**it will not leave**_**.**

**Before I begin, I should say that I **_**love **_**Doctor Who. I've watched most of the episodes, read a few of the books, I have my own replica sonic screwdriver and I can't help but grin every time I hear a TARDIS ringtone.**

**I'm also a huge fan of Transformers Prime. I watched the other incarnations of the show and always thought that they were 'okay'. Then I saw Transformers Prime, and I was hooked. The third season was a bit hinky to me, but I blame budget cuts.**

**Now don't expect this story to be as long as a few of my others. I'll honestly be surprised if it makes it to 10 chapters. This will be just a small part of the Doctor's life, after all, and I mean to make it fit within the 'Whoniverse'. **

**With that said, Allons-y!**

Blue Box, Blue Bots

Chapter 1

It Starts with a Box

**Jasper, Nevada**

Jack Darby had tried very hard to keep his head down over the last couple years of his 16-year life. He stayed out of trouble, did his chores, studied hard in school and was generally well-behaved. This was more than a desire to be a good person, or even just to fake it in order to get a bigger allowance from his mother.

Although, in his defense, it was hard for him to look like he was up to no good; he was tall for his age, yes, but he was also scrawny, with a mop of unruly black hair on his head and generally unassuming face. Like most days, he also helped the look by wearing faded jeans, a dark-gray t-shirt over a light-gray long-sleeved shirt.

If he did something stupid, he might not reunite with his best friend in the universe. In fact, said friend had given him a friendly warning the last time they'd parted.

"_You're a good kid, Jack," _he'd said, _"Keep staying good, and I won't have to do what I do to bad people."_

It was a joke, of course; he'd never hurt Jack. Still, Jack would never risk not travelling with him again. His mother felt the same way; June Darby had turned down several offers to go to better, bigger hospitals in other states, because she didn't want to risk something happening to her or Jack, not just because she was protective, but she didn't want him to think that she and Jack had abandoned him.

Of course, all that had changed when Jack got distracted by a motorcycle painted in a familiar shade of blue. After that, he'd gotten caught up in a war between two factions of giant alien robots, called Cybertronians from the planet Cybertron: the Autobots, champions of freedom and peace, and the Decepticons, who fought out of greed and all-around evil.

Jack had been scared, of course; what sane person wouldn't be terrified of giant robots that could level a city block with one servo tied behind their backs? Still, he'd been through stranger things over the years, some of which made the war between the Autobots and Decepticons look like a mild disagreement.

His Human friends, Miko and Raf, didn't know about that, however, and neither did the Autobots. He wouldn't tell them, either; he doubted they'd believe him anyway.

As he finished his shift at his job, the KO Burger fast-food restaurant, he spotted a familiar motorcycle, her blue paint giving him another pang of nostalgia, just like every time he saw her.

"How was work?" the motorcycle asked, the female voice coming from within the chassis.

"Same as usual, Arcee," Jack answered casually, as he put on his helmet and got on the seat, "Greasy food, low pay and jerks who try to take their food without paying for it."

Underneath him, Arcee shuddered slightly. "Once again, I'm glad that I don't have to go through that."

"You're a real beacon of sympathy, you know that?" Jack said sarcastically. He and Arcee had developed a system of verbally sniping at each other, but the comments were never meant to hurt; it was just how their friendship worked.

"Hey, if it makes you feel better, I have to wait out here in the hot sun while you work," Arcee said, gunning her engine and driving herself and Jack to the outskirts of Jasper, towards the Autobot base.

Jack only rolled his eyes behind his helmet. "By the way, Mom said that she was going to come over to the base after her shift at the hospital."

"Why?" Arcee asked, "Not that I mind her being around as much, but she's been a little… clingier than usual."

Jack sighed. Both he and his mother acted differently around this time of year; it was around this time, a few years ago, that they'd last seen him.

"It's just close to a time when we last saw a friend," Jack said, "We both miss him, but we don't know when he'll be back… _if_ he'll ever come back."

Arcee wanted to ask her young partner more, but from the Human's tone, it was a sensitive subject. Not like her issues with her archenemy, Airachnid, but more like a wound that had left a scar. She decided not to pursue the topic for now, but if either Jack or his mother started acting any worse, she'd speak to Optimus about it; the Prime always seemed to know what advice to give.

The rest of the ride towards the base was spent in comfortable silence. As the pair approached a large mesa, it looked like they were about to run right into the wall, but neither of them were worried. Seconds before they would have hit, a section of the wall split right down the middle and split apart, allowing them entry into the missile-silo-turned-base.

As Arcee slowed to a stop, Jack got off, allowing his partner to return to her other form. Accompanied by the sound of shifting gears and sliding plates, Arcee went from motorcycle to twenty-foot robot in only a moment. In her robot-form, Arcee had a very humanlike, hourglass figure, her arms ending in delicate-looking hands, while the lower half of her legs had a motorcycle wheel on each heel. Her coloring had remained the same: dark-blue, unpainted but polished steel, and a little dash of pink on her wrists and the sides of her helm, as well as the crest that rose above it. Her face seemed to be made of mercury, though the circuitry in her optics gave her face a more robotic element to it. Her mouth tilted upwards in a slight smile as she stretched out.

"Finally," she sighed, "driving is one thing, but being stuck in vehicle-mode for so long makes me ache."

"You never complain when you stay in my garage," Jack commented.

Arcee grinned down at her partner. "I… may have had Ratchet groundbridge me back to base every once in a while."

Jack gave a mock-scoff. "And I thought I could sleep peacefully, knowing that you'd be there to keep me and my mom safe."

"Sheesh, would you two stop acting like an old married couple or something? It's making me sick!"

Both Jack and Arcee turned to see Miko Nakadai, one of the other Humans who frequented the base. The young Japanese transfer student was wearing her usual outfit of blue shorts, purple stockings, black boots and light-purple shirt to accompany her black hair with pink highlights. She had one hand on her hip and looked at the pair in annoyance.

"What, like some people don't get tired of the best-friends-slash-sibling relationship between you and Bulkhead?" Jack asked.

"Hey, me and Bulk are just awesome like that!" Miko protested, just as her own Autobot partner walked in.

"What's this about me being awesome?" Bulkhead boomed as he walked into the room. Unlike Arcee, whose appearance belied how deadly she really was, Bulkhead was almost impossible to underestimate. He was huge, almost half again as tall as Arcee, but many times wider and heavier. His armor, which gave him an almost rotund appearance, was olive-green with black and silver highlights. Bulkhead was the second-largest Autobot on the base, but possibly the strongest and toughest.

While he lacked grace in any sort, and tended to break things by accident, Bulkhead was more than just dumb synthetic muscle. While no one underestimated his physical strength, he was much smarter than he led on. He was a master architect, able to plan out complex structures; in fact, he was the one who had expanded the base to allow giant robots to comfortably walk through it.

"Oh nothin', Bulk," Miko said, "Just saying how we're the baddest Human-Autobot duo on the planet!"

Bulkhead grinned, then reached down and placed the teen girl on his massive shoulder. "Of course we are!"

Arcee and Jack smiled at the exchange. Bulkhead and Miko had gotten along almost immediately after meeting. Of course, Bulkhead was more responsible than his young charge, and often tried to prevent Miko from getting into trouble. That almost never worked, but then again, Bulkhead was always ready to get her _out _of trouble as well.

"So, where's Raf and Bumblebee?" Arcee asked.

Bulkhead jerked his thumb over his shoulder—the one that didn't have Miko on it—to point down the hallway he'd just come from.

"Playing videogames, like usual."

"That kid needs to get out more," Miko said dryly.

"He hangs out with giant alien robots," Jack said, walking towards the main room of the base, "I'd call that getting out more."

"He hangs out with giant alien robots, only to play videogames!" Miko retorted, as Bulkhead turned around to go back the way he came, "I swear, next time a concert rolls through, I'm taking him with me!"

"That might not be a bad idea," Arcee commented, catching up to Jack in just one step, "You kids need to do some normal Human things once in a while, if only to get Jack's mom from pestering me about it."

Jack resisted the urge to grimace. His mom only did that to throw off suspicion; to be honest, a lot of the stuff Jack did with the Autobots was tame in comparison to some of his other adventures. He felt guilty about keeping secrets from his friends, but even with them, there were some things they would think were impossible or insane.

The two Autobots and their Human friends walked into the main room of the base, where they found the usual familiar faces.

First was the only other Human in the base, Rafael Esquival. Clad in his usual black, baggy pants, tan, long-sleeved shirt and orange vest, all of which seemed a size too large for the small kid, he was happily playing videogames on the couch in the area set aside for Humans. Jack had to admit that Raf was an excellent gamer, able to push his large, square-rimmed glasses further up on his face with one hand, yet not missing a beat. Not for the first time, the twelve-year-olds brown, spiky hair reminded Jack of an anime character.

"Hey guys," Raf said, barely glancing in their direction, "Welcome back."

Behind the couch, using his controller wirelessly, Bumblebee beeped a greeting. The yellow-and-black scout was the second-smallest Autobot on the team, only larger than Arcee. He was more Humanly-proportioned than Bulkhead, though he had one less finger than the other Bots and the doors from his car-form looked like wings and had his mouth concealed by a mask. He had lost the ability to speak normally, thanks to an injury at the servos of the Decepticon leader, Megatron, and could only speak in beeps and clicks, which only the other Autobots—and for reasons that no one could explain, Raf—could understand.

"Hey, 'Bee," Arcee said, waving a servo in greeting, "Anything new happen while Jack and I were out?"

Bumblebee shook his head and made a whirring sound. Arcee sighed.

"No activity from the 'Cons in almost two weeks," she groaned, "Not since that thing with the Polarity Gauntlet."

Bulkhead resisted the urge to shiver, if only because he didn't want Miko to fall off of him. That mission had not been fun; he and Arcee had been magnetized together while looking for an ancient Cybertronian relic, then almost killed. Things had worked out in the end, but it still wasn't his most pleasant memory.

"Hey, look on the bright side," Jack said, "It means less grumbling from Ratchet."

"I heard that!" a cranky voice said from across the room, though the voice's owner didn't look up from his position at a computer terminal.

Ratchet was a medium-sized Cybertronian, white with orange highlights. As appropriate for the Autobots' medic, his vehicle-mode was an ambulance, though he rarely transformed, preferring to stay at the base. Like Bumblebee, he was almost identical in proportion to a Human, though his major difference was the backpack-like addition on his back. Ratchet was old, even by the standards of a race that lived for millions of years. He was also gruff and grouchy, and though he would go offline before admitting it, he had a certain fondness for the Humans under the Autobots' protection.

"While it is unwise to drop our guard at any time," a deep, noble voice said as its owner entered the room, "Jack is correct in that we should look for the positives."

The largest Autobot on Earth, Optimus Prime was both imposing and inspiring. Though taller than even Bulkhead, he had none of the bulk, moving with surprising grace for a being his size. His legs, arms and helm were painted blue, while his chest and back were red. To Jack, he almost resembled a medieval knight, if said knight was a robot.

When Optimus' face was exposed, like now, several emotions always seemed to be present. There was wisdom, courage, determination and kindness; on top of that, the Autobot leader seemed to radiate an aura that made people trust him with anything. Anyone who was on his side would follow him to the end of the universe and back.

The effect was so great that Jack almost spilled his secret to the Last Prime, but the fact that someone else had had that same effect on him had given him a form of immunity to that kind of influence. That didn't mean that he didn't respect Optimus with all his heart, but he was still wary; some secrets were not his to share.

"Did you discover anything on your patrol, Optimus?" Ratchet asked.

The Prime shook his head. "Unfortunately, there was no sign of either Decepticon activity or Energon deposits."

The primary reason for the Autobots and Decepticons to stay on Earth, Energon was a blue crystal that had been deposited on the planet for storage by both sides eons ago, during the war on Cybertron. It served as their fuel, ammunition and medicine, and Earth was apparently chock-full of the stuff.

Sadly, the greatly-outnumbered Autobots lacked the materiel and numbers to adequately search for the precious fuel, and often had to risk attacking Decepticon mines because they couldn't mine it themselves, and at the moment, they were starting to run low.

"We will resume our search for more Energon tomorrow," Optimus declared, "For now, I suggest we take advantage of this respite and rest."

"Sounds good to me," Arcee said, strolling over to where Raf and Bumblebee were and idly watched their game.

Miko and Bulkhead went over to Raf's laptop, which he'd set up for them to use while he was playing videogames; they were soon happily watching a demolition derby online.

For his part, Jack was uncertain what to do. While it wasn't the same as his other adventures, he actually enjoyed the excitement of the Bots' missions, even though he pretended that he felt the complete opposite. In truth, he was now very, very bored.

"Jack," Optimus said quietly—for a giant robot, anyway—as he kneeled in front of the teen, "Is something troubling you?"

For a brief second, Jack panicked; had he given something away? He considered outright denying it, but then dismissed that idea; Optimus was too sharp not to notice, and Jack respected the Prime too much, so he settled for a vague truth.

"Nothing serious, Optimus," he said, "It's just that a friend of me and my mom disappeared around this time a couple of years ago. If Mom and I act weird for a while, it's just because we miss him."

"Do you fear for his safety?" Optimus asked, looking concerned.

Jack shrugged. "He tends to get himself into trouble, but he always gets out of it. I'm sure he'll show up again; he gave his word, and there are some things he won't lie about. Still… Mom and I miss him."

Optimus nodded in understanding. There were many Autobots, now scattered across the cosmos, whom he wished he could see again.

"Very well, Jack," he said, standing up again, "Speaking of your mother, was she not supposed to visit today?"

Jack quickly checked the time on his phone. "Yeah, she'll be here pretty soon, I think."

As if on cue, the proximity-sensors went off, alerting the base of an incoming vehicle. Ratchet barely glanced at it.

"It is Nurse Darby," he announced, then went back to whatever he was doing.

A minute later, June's somewhat battered white car pulled into the base, and then June stepped out. For a woman approaching forty, June looked much younger. She was fit, with the body of someone ten years younger, with healthy skin and black hair. As usual, she wore a greenish-yellow jacket over her nurse's scrubs.

"Hi, everyone," she said, waving at the Autobots and the kids, then went to hug her son. "How was your day, Jack?"

"Same old, same old," Jack replied, then noticed the nearly invisible pain in his mother's eyes and gave her another hug.

"Thanks, honey," June said, "It gets harder every year."

"You know him, Mom," Jack said, trying to lighten the mood, "He always comes back; his sense of time just stinks, that's all."

For a second, mother and son seemed to share a silent conversation.

_Be careful what you say, _June warned with her eyes.

_What? I didn't say anything specific, _Jack shot back.

The family then stepped back from each other and tried to relax, making small-talk with the Autobots or Miko and Raf, but anyone who paid attention—which was everyone except Miko and Ratchet—could see the tension in their eyes. However, no one had enough information to do anything about it, and even if they did, the base's suddenly-blaring alarms would have stopped them.

"Ratchet?" Optimus looked questioningly at the scientist, who was now typing furiously at his keyboard.

"I'm not sure, Optimus," Ratchet admitted, "I'm detecting an unknown energy-signature—it's like nothing I've ever seen!"

"Where is it?" Arcee asked.

Ratchet typed for a few more seconds, then turned around, optics wide.

"Right here."

Immediately, the other Autobots formed a circle around the Humans, their servos shifting into Energon-blasters of varying size.

"Autobots," Optimus ordered, "until we know what is happening, do not let the Humans out of sight."

Everyone in the base, Human and Autobot, were somewhat unnerved; the base was supposed to be shielded from detection, yet something had not only found them, but was apparently unconcerned by the giant robots that were each strong enough to take down a small army.

Jack just hoped that it wasn't Megatron or the Decepticons. If they had a way to detect and bypass the Autobots' defenses, then the 'Bots were as good as scrapped.

Then they heard the noise. It started out soft, but grew in volume. It was a groaning, wheezing sound that seemed mechanical, but at the same time, it sounded almost alive, fading then returning, like a breath or a heartbeat.

For the Autobots, Miko and Raf, they became even more tense at the noise, but for June and Jack, it was a signal to relax. The Darby's made their way out of the defensive circle, following the sound.

"Jack, June, get back here!" Arcee snapped, "You don't know what's coming!"

"Actually, we do, Arcee," Jack said, "It's an old friend, coming to visit."

The Autobots wanted to ask Jack what he meant, but then they saw it. It was fading in and out, as if still attempting to become solid, though everyone could now make out the rectangular shape.

"What is it?" Raf asked.

June smiled, though she didn't take her eyes off the materializing box. "Something old, something new, something borrowed, something blue."

Finally, with a dull thud, the box settled on the base's floor. It was almost ten feet tall, seemingly made of wood and painted a deep, vibrant blue. At the top of its pyramidal roof, a single light was shining. Near the roof, over the door were the words 'Police Public Call Box'.

For a moment, the box just sat there, unmoving. June took that moment to cross her arms and start tapping her foot, something she did when she was annoyed by something or someone.

Finally, the doors opened, and a man strode out. He was tall, but very skinny, with dark, barely tamed hair and a handsome face. He wore a blue suit, a white shirt and a dark-blue tie; over all that was a long, brown coat that ended at his ankles. Oddly enough, he wore a pair of Converse sneakers with the rest of the outfit.

For a few seconds, the man's eyes roamed around the base, taking in the astonished Autobots with less of the usual amazement, and more of just interest. Finally, his eyes rested on Jack and June, the latter of whom was still tapping her foot.

"The Darby family!" the man cried out in a British accent, then dashed over to them. "You've certainly found some excitement while I was gone!"

June tried her best, but she couldn't quite keep the smile off her face. "Well, we try."

The man grinned, almost maniacally so, and wrapped the mother and son in a group hug.

"We missed you too," Jack wheezed, the breath driven out of him by the man's grip, but didn't seem upset.

Optimus was first to snap out of his shock. From the way June and Jack were reacting, this was the friend who had been missing, and didn't seem to be a threat. Then again, he had bypassed several meters of stone and metal with ease, using something that not even Cybertronian technology could identify. This was concerning.

"Who are you?" he asked.

The man looked up at the Autobots, his smile still on his face. He let go of the Darby's and held out his hand; he looked like he wanted to shake hands, then did a double-take between his hand and Optimus, and settled for a wave.

"Hello," he said cheerily, "I'm the Doctor."

Miko poked her head around Bulkhead's leg and blinked a few times before speaking.

"Doctor Who?"

**And there you have it, folks! Now, as readers, I ask you to do one thing for me: if I screwed up during this chapter, or at any point during the story, **_**please **_**let me know ASAP. I'm trying my best to get the facts right about both Doctor Who and Transformers, but I can't claim to know everything about either. I just like them enough to write a crossover. However, if you find I messed up, please let me know **_**politely**_**, so that I can fix it. I listen to you guys, I really do!**

**Second thing I want to mention: this is not, I repeat, **_**NOT**_**, a Doctor/June romance. I'm trying to keep the Doctor Who storyline intact. The Doctor and June are just good friends, like how he was with Donna.**

**Next thing: you won't see any other companions in this story. It takes place during the adventures that the Tenth Doctor spent alone. Again, this is to account for the show's timeline. If anything, I'm placing the Transformers-verse into the Whoniverse, rather than just mixing them up.**

**For those of you wondering: yes, June and Jack spent time traveling with the Doctor, but no, I was never going to start out with the beginning of their adventures. This is kind of like what the Eleventh Doctor did with Rory and Amy; he dropped them off at home for a while.**

**Another thing: yes, this chapter was fairly short, but I try to keep all of my first chapters below 5000 words. Don't worry, the rest of the story will have longer chapters.**

**Next chapter, secrets are revealed, and the Decepticons are introduced to the Oncoming Storm.**

**I'm the Muffin.**

**Muffin Who?**


	2. An Explanation and an Engagement

**DOCTOR WHO DOES NOT BELONG TO ME. TRANSFORMERS DOES NOT BELONG TO ME. EVERY NIGHT, I WISH FOR A TARDIS, BUT I NEVER GET ONE. IT MAKES ME SAD.**

**Okay, I just saw the first episode of the new season of Doctor Who. All I can say is this:**

**GIVE ME MORE.**

**That is all.**

Blue Box, Blue Bots

Chapter 2

An Explanation and an Engagement

**Autobot Base**

"Doctor Who?"

Jack and his mother smiled at each other. No matter how many times they heard it over their adventures with the Doctor, that never got old. For his part, the Doctor only smirked; that question never ceased to amuse him.

The Autobots, however, were not so amused, if the stomping form of Bulkhead was anything to go by.

"She asked you a question, fleshy," the Autobot growled.

The Doctor raised an eyebrow. "Fleshy? Come now, there's no need for name-calling; I don't call you rusty, now do I?"

Bulkhead's optics narrowed at the man, but Optimus stopped him by placing a servo on the green 'Bot's shoulder.

"Bulkhead, perhaps we should let our guest explain himself."

"And maybe Jack and June can explain how _they _know _him_?" Arcee asked, giving a pointed look at the Darby family.

Jack grimaced; this was an encounter he'd hoped to avoid. Arcee was very protective, but also didn't take betrayal—real or perceived—very well.

The Doctor, on the other hand, actually looked pleased. Now that June thought about it, he probably was; the man loved to talk, especially about himself.

"Shall I start at the beginning?" the Doctor asked, then began, without waiting for an answer. "Well, like I said, I'm the Doctor—_just _the Doctor. I'm a Time Lord from the planet Gallifrey, and I've come to see my friends, June and Jack Darby, as well as see if there was anything interesting. Turns out, there is: you lot! Now, who are you?"

The Darby family was fairly surprised; something must have happened, because the Doctor tended to ramble a bit more than that. Then they saw it; it was faint, barely a flicker in the Time Lord's eyes, but they could see suppressed grief, anger and pain. Whatever had happened had reduced him to a fraction of what he used to be.

The Autobots, along with Miko and Raf, were somewhat stumped by the Doctor's words. Really, what _could _you say to someone who called himself a Time Lord and considered giant robots only 'interesting'?

To his credit, Optimus Prime only blinked his optics once before answering. "I am Optimus Prime. We are autonomous robotic organisms from the planet Cybertron, otherwise known as Autobots."

Finally, the Doctor had a look of surprise on his face. That quickly morphed into a wide grin as he looked at June.

"Cybertron, did he say _Cybertron_? Oh, that is brilliant! I've been wanting to meet a Cybertronian for years, but Primus never gave me a chance; cheeky guy time-locked the whole planet, just so that I wouldn't pay a visit."

"Whoa, whoa, whoa!" Bulkhead said, holding up his servos, "Back up! You're saying you met _Primus_!? Our creator, being of order—_that _Primus!?"

"Oh, yeah," the Doctor said dismissively, "I met him not long after he made the Thirteen Primes. You look nothing like them, by the way—both them and Primus looked more like they were made of stone, or like those early metal tools used by Humans. You lot are much nicer to look at; the last few hundred-million years have been kind to you, haven't they?"

"Not counting the civil war, of course," Jack said in an aside.

The Doctor turned to face him, his smile gone in a flash. "War? What war? Before I was kicked out, Primus and the Thirteen were setting up one of the most stable systems of government I've ever seen. How could a civil war spring up from that?"

June realized what the Doctor had done and sighed; he'd deflected the questions about himself by distracting everyone with questions of his own, or by referencing past exploits, thus avoiding any discussions about his origins. It had taken her and Jack almost two weeks of traveling with the Doctor to get the whole story; she doubted that the Doctor would be telling the 'Bots everything in the probably short amount of time he would be here.

"Doctor," she said gently, knowing how much he hated to be interrupted, "Why don't Jack and I tell them about how we know you? I know how you hate to go into the details, and you can hear it from _our _perspective, though I might need the Doctor to pitch in every once in a while. There were a couple of things that only he saw."

The Doctor paused and frowned thoughtfully. Now that he thought about it, he rarely heard things from his companions' point of view, unless they were informing him of things they'd discovered, and even then, he usually ignored them if they weren't relevant to the situation at hand. Listening about how they met him from their eyes would certainly be different, and he loved different. Besides, while June told the story, he could observe these 'Autobots' and see what other changes had occurred to their race.

"Yeah, all right," he said cheerfully, "Why don't I make a spot of tea first? D'you still take it with two sugars, June?"

"Thank you, Doctor," June said, smiling; even after all this time, the Doctor still remembered how she liked her tea.

The Doctor grinned back, then dashed for the blue box he'd arrived in. He opened the doors and ran inside; a few minutes later, he came back with not only two cups of tea, excellently balanced on one hand, but also a comfortable-looking couch that _floated two inches off the ground_!

"Thought I'd make this more enjoyable," he said, stopping the floating couch's movement a short distance away from the group, "I got this couch as a gift from the Chancellor of Egypt after I found out who was trying to blackmail him—it was his Vice-Chancellor, of course."

"Egypt doesn't have a Chancellor," Raf said uncertainly.

"It will in seven thousand years," the Doctor said, handing June her tea and sitting down on the couch, "Now then, everyone get settled, Mother's going to tell us a story."

If June hadn't been sipping her tea—it was delicious; the Doctor always had the best teas—she would have swatted him.

Instead, she only glared at him, then began speaking. "Well, it started three years ago. Jack and I acted quite differently back then. In fact, you wouldn't have recognized us then…"

…

**Three years ago**

"Jack, please slow down!" June called after her son as he raced to the car. The twelve-year-old had tears running down his face and refused to tell her why. That combination was doubly worrying for the boy's mother.

"I don't want to talk about it!" Jack shouted, briefly turning his head to address June.

That moment of not looking where he was going was all it took for Jack to accidentally run into someone, the impact sending the boy falling backwards.

"Jack, are you okay?" June asked worriedly as she helped her son to his feet, then turned to the person he'd run into. "I'm so sorry, are you… okay…?"

June trailed off at the sight of who was standing in front of her and Jack. Whatever it was wasn't Human, that was for sure. It was roughly five feet tall with a wide torso, a brown-skinned, leathery head that vaguely reminded June of a potato. It wore a dull-silver suit with a blue collar, shoulders and belt. In its three-fingered hands was a device that was quite obviously a weapon.

A weapon that was now aimed at her son.

Immediately going into mother-mode, June grabbed Jack and pushed him to the side, but putting herself in the line of fire as the weapon made an ominous humming sound. June closed her eyes, expecting the end, her only regret being that she wouldn't be able to watch Jack grow up…

Just as the strange creature pulled the trigger, another, more high-pitched noise was heard, and the weapon sparked madly, but did nothing else.

June opened her eyes just as a man wearing a blue suit ran up, a small silver tube that had a glowing blue light on one end in his hand. He placed himself between the creature and the terrified mother and child.

"You!" the creature shouted angrily, "You interfere in our plans again, Doctor!?"

"Yes I do," the man—the Doctor—said sternly, "Your invasion of Earth failed, Sontaran, so why are you still here? There's nothing left for you to do!"

The creature, apparently called a Sontaran, scoffed. "You may have stopped our primary method, but we _will _conquer this world. You know that we will never give up, Doctor!"

The Doctor sighed as he put the silver tube into a pocket in his jacket. "I know. You lot never give up until you die… that's why I've overloaded your weapon. It'll explode in thirty seconds unless you tell me where the rest of you are hiding; if you do that, I'll let you go."

"You are bluffing, Doctor!" the Sontaran said accusingly.

"Am I? I blew up your ship and that was filled with thousands of your people. Compared to that, one more soldier is easy."

The Sontaran raised his weapon again. The Doctor spared half a moment to sigh, then turned around to grab Jack and June by the hand and pull them along.

"Run!" he shouted, directing them behind a car just as the Sontaran pulled the trigger. Instead of firing, the weapon exploded, completely incinerating the Sontaran, leaving just a black scorch-mark on the ground.

The Doctor looked at the smoking spot and sighed. "I didn't want that to happen. Now I don't have any leads for where the rest of them are!"

He angrily kicked the tire of the car he'd been using for cover, then started to pace, muttering under his breath. It was then that Jack's brain got his mouth to work again.

"There are more of those things?" he asked.

"Hm?" the Doctor looked at the Darby's as if he was noticing them for the first time. "Oh, probably no more than five or six. That's all that could have escaped before the ship exploded. I thought I got them all, but it turns out I missed a few."

Now it was June's turn to get her mouth working. "You just saved our lives."

The Doctor nodded. "Yes, yes I did."

"Thank you," June said sincerely.

The Doctor blinked. "No trouble. It's what I do… well, it's what I try to do."

For an instant, June could see a flash of pain in the man's eyes; it was the kind of pain that, had it happened to Jack, she'd have wrapped him in the biggest hug she could give.

"Well, thank you anyway; I'm June and this is my son, Jack, and, uh… I'm sorry, I don't even know your name."

The Doctor brightened up a bit. "Right, I didn't introduce myself, did I? I'm the Doctor."

"Doctor Who?" Jack asked.

The Doctor grinned. "Just the Doctor. Now, it was lovely meeting you, but I have to go—there are more Sontarans to stop, and I don't think I have a lot of time to stop them."

With that, the Doctor turned around and dashed off towards a blue box that was sitting in the middle of the parking lot. June blinked; she was certain that that hadn't been there before. The Doctor opened the door and ran inside. He came out a few seconds later, holding a strange device that looked like a cross between a handheld radio and something out of Dr. Seuss.

"What's that?" Jack asked, pointing at the device.

"Oh, this?" the Doctor smiled. "It's my timey-wimey detector. It goes ding when there's stuff."

Jack and June looked at the device, then at each other, not knowing what to say. What _could _you say to something like that?

The Doctor pulled out the antennae on the device and started waving it near where the Sontaran had stood. A moment later, the device let out a _ding_, much to the Doctor's pleasure.

"Got it," he said happily, then pulled out the silver cylinder from before and pointing the blue light at it. After a moment, he held the silver tube to his ear, as if listening to something, then pointed it at the strange device again. Said device then dinged several times in rapid succession.

"Great, I picked up the trail," he said, then headed off in a seemingly random direction. "Nice meeting you, June, and you too, Jack. Allons-y!"

And with that, he was gone. June wasn't sure if she was going insane or if the Doctor was, but she decided then that she was going to get Jack home, and then call the police. She turned to grab Jack's hand, but…

"Jack? Jack, where did you go!?" then she spotted the Doctor in the distance, a small, familiar form trying to follow him without being noticed.

"Oh, he is _so _grounded…"

…

Jack considered himself quite clever, and to an extent, he was right. He was cleverer than the average twelve-year-old, but against the Doctor, he had no chance. He had only been tailing the strange man for a few minutes before he stopped walking and turned around, an expression that was equal parts amused and annoyed.

"I'm about to run headlong into who knows what kind of danger," he said sternly, "This is the last place for a child your age."

"I'm old enough!" Jack protested, even though he had no idea what he was old enough for, "I'm almost thirteen!"

"Good for you," the Doctor said sarcastically, "Come back when you're five _hundred _and thirteen and we'll talk."

The Doctor turned to leave, but then he heard a pitiful sniff. He glanced over his shoulder and saw Jack trying to hold back tears. The Doctor walked over to the boy and knelt to get a good look at Jack's face.

"Have you been crying?" he asked, noting the tracks on the boy's face.

"No," Jack said, stubbornly trying to keep his face hidden behind his hands.

"That was a very bad lie," the Doctor said gently, "And just so you know, I'm a master liar, so I know what I'm talking about. Now, why were you crying?"

Jack looked away. "The kids in school said I couldn't hang out with them because I'm the youngest. It's not fair; they haven't been thirteen for very long!"

At first, the Doctor looked around for the boy's mother, but didn't see her. Then he thought about it for a moment, and made a concession.

"Okay," he said reluctantly, "If you do _exactly _as I say, you can come with me."

Jack smiled, but the Doctor was as stern as his mother as he continued. "That means that if I say hide, you hide and don't move until I come get you, and if I say run, you go back the way you came and you don't stop. Do you understand me?"

Jack saw the look in the Doctor's eyes and nodded. He wasn't the type of person to break a promise, so if the Doctor told him to do something, he'd do it.

The Doctor smiled. "Good. All right then, Jack, let's go!"

The two dashed off, unaware that there was an irate mother hot on their trail.

…

The Doctor and Jack followed the timey-wimey detector in silence for a few more minutes. In the Doctor's opinion, Jack was fairly athletic for a boy his age; most people had trouble keeping up with him for more than a few minutes, but the child was doing so without complaint. It was something he rarely encountered with the Americans he met—they were always complaining about something.

Finally, the pair ended up at a large warehouse that looked to be abandoned, if the cracked and dusty windows were anything to go by.

"What is this place?" the Doctor asked.

"It's a warehouse," Jack said, as if it were obvious.

"Oy, _I _make the cheeky comments 'round here," the Doctor snapped, though there was no malice in his tone; if anything, he sounded amused. "What was this warehouse used for?"

Jack shrugged. "I don't know. It's been like this since I was little."

The Doctor shrugged back. He supposed that it wasn't important anyway, and if it was, he'd find out.

"There you are!"

Both the boy and the man jumped at the voice behind them and turned. Standing there, panting for breath, was a furious June Darby. From the way that Jack suddenly hid behind the Doctor, the Time Lord assumed that June's wrath was not something you wanted to be on the receiving end of.

"Jackson Darby," June growled, marching forward and grabbing Jack by the arm, "You are coming home with me right now and I am calling the police."

"Um, that might be a bad idea," the Doctor said, "Sontarans are rather violent, if you recall, and I'd prefer to keep Human casualties to a minimum."

"And does bringing my son into a dangerous place count as the 'minimum' number of casualties!?" June demanded, outraged.

The Doctor flinched, then took a deep breath and looked June in the eyes.

"June, I swear on my life that Jack was never going to be in any danger. If I thought he would be, I'd have sent him back and kept him protected the whole way. He just wanted to be part of something because the other children didn't want him around."

June looked over at her son, who was looking down shamefully. "Jack, is that why you were crying?"

Jack nodded. "Sorry, Mom."

June's heart broke at the pitiful voice coming from her son and held him close. "Oh, Jack, I'm sorry. Kids can be mean, I know."

The Doctor watched the hug go on in silence for a few seconds, then clapped his hands once. "Well, since you're here, why don't you come with us?"

June looked at him strangely. "Excuse me?"

"Well, I could use an extra pair of eyes in there," the Doctor said, gesturing towards the warehouse, "No offense to Jack, but adults make for better company in dangerous places—they don't scream as loudly."

"Hey!" both Darby's said at once.

"That being said, we can't waste time," the Doctor continued, "Right now, you have to make a decision: do you want to stay here, where it's safe, or do you want to come with a madman whom you just met into a place that might be filled with danger and possibly save the planet?"

June started at the words 'save the planet'. "These Sontarans… are they really that bad?"

The Doctor nodded solemnly. "They never miss a chance to fight a war, and Humanity put up a bit of a fight last time. We can't let these survivors tell the rest about what happened; it'll just draw more here, and I got very, very lucky the last time."

"What do they want?" Jack asked.

"They wanted to turn Earth into a breeding ground for more Sontarans. Unfortunately, they were going to kill every Human on Earth to make room."

"Why would they come here?" June wondered aloud.

The Doctor shrugged. "The planet has resources, and for some reason, you Humans just seem to have really bad luck when it comes to alien invasions."

"You talk as if you're not Human," June said.

The Doctor nodded. "That's because I'm not. I'm a Time Lord from the planet Gallifrey. I'm nine hundred years old, I travel around the universe in a blue box and I've been saving the Human race for centuries.

"Still want to come with me?"

June looked down at her son, who nodded. She grabbed him by the shoulders and forced him to look at her.

"Jack, I want you to stay here."

"But Moooom…"

"No buts, mister," she said, "I am _not _putting my son in danger on the word of someone I just met."

"What about _you_?"

June glanced at the Doctor, who was trying to look like he wasn't paying attention to every word they were saying, but failing miserably.

"I'll go with the Doctor to find out if he's telling the truth," she said at last, "But I'll be right back. If I don't… if I'm not back in ten minutes, I want you to call the police, okay?"

_Besides, _she added in her mind, _if the world really is in danger, isn't it my duty as a citizen of the world to at least check it out?_

Jack briefly looked at the Doctor, who nodded and shot him a thumbs-up. He sighed.

"Okay, I'll stay, but you better come back. You _will _bring her back, right, Doctor?"

The Doctor nodded again. "I swear on my life that I will bring your mother back to you, Jack."

With that, Jack took a few steps back to hide behind some bushes, while the Doctor and June approached the warehouse. As soon as they were close, June pointed at the door.

"It's locked."

"Don't worry," the Doctor said, pulling out the silver tube again, "I have a key."

"What _is _that thing?" June asked.

"Sonic screwdriver," the Doctor said, pointing it at the lock; a second later, some sparks flew, and the padlock fell to the ground.

"It's great for opening doors," the Doctor added with a smirk.

"And blowing up guns, right?" June said, remembering how the Doctor had defeated that first Sontaran, "Is that why you don't have a gun?"

The Doctor shook his head as he slowly opened the door. "No, I don't use guns because once you have one, you tend to think that all your problems can be solved with them. I'd rather solve problems by being clever."

Once inside the warehouse, it didn't take long for June to realize that something was wrong. "This place has been abandoned for almost fifteen years, but there's no dust on the floor. It looks like someone was cleaning up around here."

The Doctor looked at the floor and realized that, indeed, it was spotless. "Yep, that confirms that something is wrong here. Look around, see if anything else is unusual—the base is probably underneath us, so look for a button or a switch or something."

June did look around, but it was an empty warehouse. There was nothing out of the ordinary, save for the clean floor. She walked forward, looking down for a button or something that might be disguised as part of the floor, but then she felt something hit her head.

"Ouch!" it was rather painful, too. "Doctor, something's here!"

The Doctor looked up from his half of the warehouse. "I don't see anything."

"But I just hit my head on it!" June protested, then moved her arms up until they knocked against something solid. "See? There's something here!"

The Doctor hurried over and ran his hands where June's had been. When he felt it, he grinned.

"Oh, optical camouflage, that's being careful. They don't have the numbers or the firepower to take on the whole planet, and they'd know that UNIT would be looking for survivors."

"Who's UNIT?" June asked.

"UNified Intelligence Taskforce," the Doctor explained, "They investigate alien… stuff. I help them out from time to time."

"Like now?"

"No, this was just something I realized I should have done a while ago." Now the Doctor looked frustrated. "Okay, I can't find the controls to turn off the camouflage; guess I'll have to do it the old-fashioned way, eh?"

The Doctor pulled out his sonic screwdriver again and waved it around, a series of clicks and pings emanating from it. A few seconds later, there was a shimmer in the air, and then a square structure, about the size of a shed, appeared in front of them!

"What… how…?" June tried to say.

"It's an elevator," the Doctor said, now applying his screwdriver to the door, "The Sontarans built their base quite a ways under the surface if they needed one of these."

When the Doctor opened the door, he gestured for June to enter, which she did, albeit tentatively. The Doctor was right behind her; he looked over at the controls near the door, then pressed a button. A second later, they felt themselves moving down.

"There's just one thing I don't understand yet," the Doctor said, more to himself than June, "Why here, in Jasper? There's not really anything of interest, no special technology or resources—why come here?"

"Maybe they didn't have anywhere else to go?" June offered, though she felt a little defensive about her hometown being called uninteresting; granted, it was true that Jasper was about as interesting as unbuttered toast, but it was still her home!

The Doctor considered that. "Well, it's possible. If they left their ship quickly, they might not have had a chance to set the navigation systems. Still, they've been here a while—they'd have to be to set up a base like this—so why didn't they just head to somewhere with more resources?"

"Well, I don't think we'll find out in an elevator," June pointed out.

The Doctor opened his mouth to speak, but couldn't refute that. He settled for looking sulky for the rest of the way down.

Once the doors opened, the two of them cautiously walked out, quickly taking cover behind a large crate. Beyond the elevator was what looked like a mine, but it was unlike any mine June had ever heard about; the handful of Sontarans weren't mining gold or metals, but strange blue crystals that sprouted out of the ground and walls and seemed to glow from within.

"What is that stuff?" June asked, trying to be heard over the sound of running equipment, but not loud enough to get noticed by the Sontarans.

"I'm not sure," the Doctor admitted, but then his eyes went wide. "It might be… no, it couldn't, they haven't been to this planet, have they? Oh dear, this is very, very bad."

"Why is it bad?" June asked crossly, annoyed that the Doctor seemed to be ignoring her.

However, before the Doctor could answer, a familiar charging sound was heard behind them.

"Raise your hands, Human vermin!" a Sontaran ordered.

Slowly, the Doctor and June raised their hands and turned to see the single Sontaran was gesturing the others over with his free hand, the other one was aiming his weapon at them. June didn't even try to stop herself from trembling, but the Doctor only looked annoyed.

"I am getting really tired of people pointing guns at me," he muttered.

…

Outside and on the surface, Jack was starting to pace nervously, occasionally checking his watch. It had been almost ten minutes, and neither his mother nor the Doctor had come back out. He looked around, but there was no sign of anything happening, either.

Jack looked down at his watch again and saw, to his dismay, that the ten minutes had passed. He reached for his phone…

Which wasn't there! Frantically, Jack looked around, but it wasn't anywhere near him. Jack smacked his forehead angrily; he must have dropped it when he'd run into the first Sontaran and hadn't realized it!

Now he was starting to panic; he could run back into Jasper, but even at twelve years old, he wasn't naïve enough to think that the police would believe that aliens from outer space had kidnapped his mother, who was travelling with _another _alien.

_Heck, _he thought, _even _I _wouldn't believe it, and I'm living it!_

He stopped pacing when he realized that the door to the warehouse was open. He remembered his mother's words, reminding him to stay out, but…

_If those aliens hurt Mom,_ he thought, his vision suddenly tinted red, _I'll destroy them!_

It was rather silly to imagine a twelve-year-old fighting and _defeating _an unknown number of trained soldiers, but children that age still believed in their own invincibility. Besides, Jack was too angry to care.

Without a second thought, he sprinted for the warehouse, only stopping for an instant when he saw the elevator. He pushed the only available button, and the platform rose up to him. He stepped onto it and pressed the button on the inside. A second later, he was heading down.

When he arrived, he quickly dashed out and hid behind a large crate, unaware that his mother and the Doctor had hid behind the same crate just a few minutes earlier. In the distance, he could make out the shapes of June and the Doctor, marched along at gunpoint by several Sontarans. There were only two left, and they were overseeing some sort of drill that was carving a large blue crystal into small fragments. Gulping nervously, Jack stuck to the shadows and tried to draw as little attention to himself as he moved.

The only time that he was almost caught was when he tripped over a small box. Thankfully, the loud drill drowned out the sound of the impact and the cry of surprise. Jack rubbed his sore knee, then began to rise when he saw what was inside the box he'd tripped over.

Jack was by no means a genius, but he was intelligent to recognize a warning, even if it was in an alien language. This particular warning was printed on the sides of a dozen rectangular sticks, each about as long as his arm. Attached to each stick was a small device with a button on it. Jack had watched enough action-films—even if his mother didn't approve—to know a detonator when he saw one.

It was then that a plan began to form in his mind.

…

"Why aren't they shooting us?" June asked quietly, so that only the Doctor could hear.

"Do you _want _them to?" the Doctor asked back, then answered her question. "We're not armed, so we're not a threat. They'll kill us, but until we give them a reason, they'll probably just gloat a bit first."

"That's good, right?"

"Probably," the Doctor said, "It'll give me a chance to find out what they're doing, at least."

"So we can stop it?" June asked hopefully.

The Doctor shrugged. "Or at least I'll die with my curiosity satisfied."

June's mouth hung open with disbelief; dying wasn't an issue to this nut, but dying without getting answers was?

Finally, the Sontarans ordered them to halt, which they did and then slowly lowered their arms. One of the Sontarans sneered at the Doctor.

"You have failed this time, Time Lord," he said, "We shall avenge our defeat at your hands, and destroy this world that you hold so dear."

"Really?" the Doctor asked in an unconcerned tone, "I don't believe you will. I doubt that six Sontarans have enough power to take down a planet of seven billion, even if your technology is thousands of years ahead of Earth's."

The Sontaran smirked. "That is where you are wrong, Doctor. These blue crystals are dotted across the world; the tests we've run prove that they are highly explosive if heated to the correct temperature. Combined with our own explosives, if enough of the crystals are detonated in the right way—"

"The explosion could be powerful enough to knock the Earth off its axis," the Doctor completed, his eyes widening in horror. "You can't do that, billions of innocents will die! They won't be able to adapt to the change in climate in time!"

"You brought this upon yourself, Doctor," another Sontaran said, "If you had let us succeed in our plans, we would have given that Human—boy?—and all his kind a relatively painless demise."

"Human boy?" June said, looking around before turning to the Doctor. "Is he talking about me?"

The Doctor sighed. "Some Sontarans have issues with gender… it's complicated."

June wasn't sure what to be more angry about: that the Sontarans were about to commit genocide or that they couldn't tell her gender, when she was _obviously _a woman!

For his part, the Doctor was feeling a bit resigned; if he'd had more time to plan—as ironic as that statement was—he might have been more confident. Then, out of the corner of his eye, he spotted a familiar, non-Sontaran shape creeping closer. When he saw what was in the figure's hands, he had to fight a smile.

_Smart kid._

"There's just one thing you Sontarans have forgotten," the Doctor said, raising his voice.

"Oh, and what is that?" the first Sontaran asked.

The Human-looking man smirked. "I am the Doctor, the Oncoming Storm. I am the Last of the Time Lords, and I have defeated your people again and again. I will never stop fighting for this planet or the people who live on it.

"Today, however… today, I won't have to." The Doctor turned around, "Am I right, Jack?"

Jack stepped out of the shadows with a nervous expression, though he walked forward steadily and with his head held high. In one of Jack's arms, several small devices were cradled, while in his opposite hand, an identical device was held, his thumb right over the button.

"Let them go," Jack said, without the slightest tremor of fear in his voice, "Let them go now, or I blow this whole place up."

The Sontarans turned to face Jack, their weapons not quite pointing at him, but getting there. The Doctor wasn't about to let them kill a twelve-year-old, nor was he about to let that same twelve-year-old be responsible for killing anyone. In a flash, he pulled out his sonic screwdriver and pointed it at the Sontarans' weapons, temporarily disabling them; unlike the first one, he didn't have time to overload the weapons. He would have to move fast.

Thankfully, that was something that the Doctor excelled at.

He grabbed June's hand and ran towards Jack, ducking away from the arms of the Sontarans, who had thrown away their momentarily-useless weapons.

"Run!" the Doctor shouted; June slowed the Time Lord down just long enough to grab Jack by the elbow, and the three of them ran.

"Jackson Darby," June shouted, "What were you thinking!? I told you to get the police!"

"I lost my phone!" Jack protested, "And besides, would they have believed me?"

"He has a point," the Doctor said, "Would the police have taken Jack seriously?"

"Probably not," June admitted, "But still, Jack, you shouldn't have done that!"

For a brief second, Jack looked very, very angry. "I already lost one parent. I'm not going to lose the other!"

Further arguing was cut off when a bolt of energy impacted above their heads, showering them with dust.

"Well," the Doctor coughed, "Looks like their weapons are working again. Head for the elevator!"

Unfortunately, the three of them did not get very far before the barrage of fire forced them to take cover. The upside was that they were not far from the elevator, but the downside was that the second they ducked out of their cover, the Sontarans would kill them.

"What now?" June asked breathlessly.

The Doctor held out his hand to Jack. "Here, give me one of those detonators, and I'll set off a few explosions to distract them."

"Uh…" Jack looked flustered. "I didn't actually set any of the bombs."

"What!?" both June and the Doctor said.

Jack seemed to shrink in on himself. "I just grabbed the detonator things and made it look threatening. I was just bluffing!"

June sighed. "I'm not sure if I should be happy about that or not."

Then the Doctor got an idea. "Jack, where did you get those detonators from?"

Jack jerked his thumb the way they'd come. "There's a box full of them near the big drill."

The Doctor thought about that for a moment, his mind going at speeds faster than any Human could.

"Okay, we're going to have to time this right, but you both have to trust me."

The Darby's looked at each other, then nodded at the Doctor.

"We don't really have any other options, do we, Doctor?" June asked.

The Doctor smiled. "Nope! Now, Jack, give me the detonators. When I say so, I want you both to run to the elevator and for God's sake, please keep the door open for me because I will be right behind you."

Jack handed over the detonators, which the Doctor then waved his sonic screwdriver over—unbeknownst to either of the Humans, the Doctor was linking all the detonators up to one—then got into a ready position near his mother. They nodded at the Time Lord.

"Right then," the Doctor said, then pressed the button of one of the detonators, "Allons-y!"

…

"Do you hear something?" asked one of the Sontarans who had stayed behind next to the drill.

"I believe I do," the other Sontaran said, looking around, "It sounds like a beeping, much like our… demolition… charges…"

Both Sontarans turned to see an open box behind them, which was clearly marked in their own language, 'Highly Explosive'.

"It was an honor to serve the Sontaran Empire," one Sontaran said solemnly.

The other Sontaran shrugged, since he was about to die. "I always hated you."

The first Sontaran barely had time to ask 'what?' when the bombs went off. Individually, each charge would have only blown off chunks of the large Energon crystal nearby, but over a dozen going off at once generated just enough heat and force to set off a chain-reaction that began completely destroying the mine.

…

"Let me in, let me in!" the Doctor cried, diving into the elevator just as blue explosions rocked the mine.

As soon as he was inside, June hit the button in the elevator, closing the doors and sending them flying upwards.

"Can we get outside in time?" Jack asked.

The Doctor pulled out his sonic screwdriver and pointed it at the controls. "Hopefully, I can boost the speed on this thing—whoa!"

With a jerk, the elevator doubled, then tripled in speed, rising to the surface in only a few seconds. As soon as the doors opened, the Doctor ushered the Humans out.

"Run, go!" he shouted, running past them, only slowing long enough to grab their hands and pull them the rest of the way out. The three sprinted out of the warehouse and kept on running, until a massive explosion lifted them off their feet and flung them almost a dozen meters, where they rolled down a small ditch.

For a while, they just lay there, panting and trying to get their hearing to work again. Finally, the Doctor turned to June.

"Are you all right?" weakly, the nurse nodded. "Jack, are you okay?"

Jack nodded too, then started to laugh. It wasn't a laugh of humor, but a release of nervous energy, something that his mother soon joined him in. Even the Doctor let out a few chuckles.

"Is it always like this with you?" June asked.

The Doctor shrugged. "Not really. Sometimes it gets scary."

That set off more laughter from the Humans, but the Doctor only crossed his arms.

"I'm serious," he said grimly, quickly silencing the laughter. With a sigh, the Time Lord stood up and brushed the dust from his coat.

"Well, it's been fun, but I've got to get going."

"Going?" June repeated, "Going where?"

The Doctor looked as if he were considering it. "No idea, really. Come on, you two, up you get, I'll walk you back to town."

…

The walk back to Jasper was quiet. Jack and June were still processing that they could have died, but at the same time, they might have helped to save the world, while the Doctor looked to be lost in thought.

Still, they encountered no more danger as they reached the same parking lot where it all started. The same scorch-mark was still present, though all three of them tried not to notice it. Once they reached June's car, the Doctor clapped his hands together and smiled.

"Well then, safe and sound, just like I promised. Thank you, by the way."

"We didn't really do much down there," June protested, though she flushed in embarrassment, "We just ran and stayed alive."

The Doctor's smile became a little wistful. "And that is why I'm thanking you. I've lost too many people in my life, and it's nice to see the people who go with me into something all come out alive."

There was something that crossed the Doctor's eyes, so fast that it took a moment for June to recognize it as pain.

"Are you all right?" she asked.

The Doctor waved a hand dismissively. "Yeah, I'm fine. Listen, if you two are smart, you'll go home and forget all of this, and forget about me."

"How can we forget what just happened?" Jack asked, "That was amazing! Are you really an alien?"

The Doctor sighed; it was pointless trying to dodge the questions of children. "Yes, I'm a Time Lord. I'm from another planet."

"B-but… you look just like us!" June protested. If anything, the Sontarans were more alien, though the Doctor's behavior could at least be described as odd.

"Well, to my people," the Doctor said with a smirk, "You Humans look like Time Lords. Also, I've got two hearts."

Before either Darby could comment on that, the Doctor turned around and headed back into the blue box. June wasn't sure when she'd started moving, but suddenly she was in front of that box and banged on the door.

"Hey, you can't just leave like that!"

The Doctor opened the door just enough to stick his head out. "Why not?"

"Because that was fun!" Jack said, having joined his mother, "Can we do more stuff like that? Except, you know, with less people shooting at us?"

June opened her mouth to scold her son, but the Doctor beat her to it.

"No, not a chance. I travel alone now; too many people get hurt when they travel with me."

Jack crossed his arms. "Do we look like people?"

Even as those two talked, June was surprised to find that she was actually warming up to the idea. The Doctor seemed nice, if a little strange—then again, he _was _an alien—and he'd said that he protected Humanity from threats like the Sontarans. If she and her son were to travel with someone, why not someone who kept others safe?

For his part, the Doctor looked like someone had clubbed him over the head, staring at Jack in amazement. To June and Jack, he seemed to be having an argument with himself.

"You don't have to, of course," June said, "But other than the evil potato-people with guns, Jasper is a really boring town. To be honest, you're the first exciting thing to happen in our lives since… ever."

Now the Doctor looked almost angry. "What, this town doesn't have a… a cinema or something?"

Jack held up his hands and mimed weighing something. "Movies about talking cars… cool alien guy with a blue box who saves the world… kind of a no-brainer."

Under his breath, so softly that June could barely hear it, the Doctor whispered, "This is the last time…"

Then in a louder voice, he said, "Oh, all right! Both of you, get inside here, and I'll show you something cool. _One _thing, mind you; after that, I'm bringing you back here."

June looked skeptically at the box. "You want us to get in there? Not a whole lot of room."

Now the Doctor smirked. "Say that once you're inside."

A thought suddenly struck June. "Actually, maybe we should wait until this weekend? Jack has school tomorrow."

"Moooom…"

The Doctor's tone was smug. "Oh, don't worry. Not only is this box a spaceship… it's also a time machine."

June and Jack blinked.

The Doctor continued. "I can bring you to any place in the universe, and at any time, and then bring you right back to the moment you left."

In June's mind, she was suddenly a child again. This was the sort of thing that only happened to fictional characters in movies and on television, but now she and her son were faced with the chance to _live _the fantasy.

At the thought of her son, June then went back into mother-mode. "Can you be completely sure that Jack and I will be safe?"

The Doctor shrugged. "I can't be completely sure about anything, but I can do my best."

June looked at her son. "Jack, what do you think?"

Jack didn't hesitate. "Come on, Mom, this is going to be fun!"

The Doctor grinned. "Yeah, come on, Mom!"

June sent the Time Lord one more suspicious look. "Try anything funny, and you'll wish you stayed in that mine."

The Doctor held up his hands to placate her. "I promise I'll behave. Besides, it's just one trip, right?"

…

**Autobot Base, Present Day**

"It wasn't just one trip," June said at the end of the tale, "We ended up spending almost a year with the Doctor, though he did bring us back to the same moment we left."

"Wait a second," Raf said, "Something doesn't make sense. You said that Jack was twelve when you met the Doctor, but you met him three years ago and Jack is _sixteen _now."

"Oh, that," Jack said, rubbing the back of his head, "Well, the Doctor figured that people would notice if I were suddenly a couple of inches taller, so when we got back, he hacked every record of me and changed my age to fit. Biologically, I'm sixteen, but chronologically, I'm fifteen."

"Puh-_lease_," Ratchet scoffed, "Time-travel is impossible! There are paradoxes to consider, not to mention that the power requirements would be…"

"We've heard all that before, Ratchet," June said a little sharply, "The paradoxes tend to resolve themselves and the power problem… okay, the Doctor never really explained that, but I'm not sure we'd have understood anyway. Right, Doctor?"

There was no answer. The Autobots and Humans turned to face the Time Lord, but he was no longer on the couch. In fact, he wasn't even in the base anymore. The only sign of his presence was his now-empty cup of tea and a piece of paper where he'd been sitting.

"He must have left during the story," Jack said, realizing that the Doctor had stopped contributing to the tale about halfway through, then picked up the piece of paper and read aloud, "June, sorry about leaving, but I was getting bored. Figured I'd borrow your car and drive around a bit. Love, the Doctor."

"That guy has mad ninja-skills," Miko commented, a little awed that the Doctor had been able to sneak away unnoticed.

"He took my car!?" June was furious, "It's not like he ever let me fly the TARDIS, why makes him think I'd let him drive my car? Does he even have a license!?"

The Autobots were similarly mystified, but for different reasons. How could something as important as the discovery of time-travel escaped their notice? It was true that Cybertron had become rather isolated over the eons, but still…

Out of the five Autobots, only Optimus knew the truth. It had echoed through his processor as soon as that blue box had arrived, though at first, he was unsure of how he knew it. It took a while, but he traced the source of his unease to the Matrix of Leadership, which rested within his chassis. The source of the shared wisdom of the Primes, and the tenets of Primus himself, lay within, but at the moment, there was a piece of knowledge that suddenly made sense.

Primus had decreed that no Cybertronian would interfere with the workings of time itself. Time could be studied, perhaps even influenced—Alpha Trion was an example of this—but to physically travel through time was forbidden. Not even the Decepticons attempted it.

Optimus recalled how the Doctor had mentioned Primus and the Thirteen Primes as if he'd met them… perhaps the Doctor was the reason for Primus' decree?

There were far too many questions and almost no answers.

"Autobots," Optimus said, his baritone voice catching everyone's attention, "We must find the Doctor. There are things that I must know, and I believe that the Doctor is the only one who can tell me."

…

**Jasper**

The Doctor had left June's car in the same parking lot that he'd first met her, then began walking through the streets. Though he liked adventure and excitement, there was a certain charm to these boring little towns… as long as he didn't visit them often or for very long.

There wasn't too much to hold his attention, and the occasional person he met only looked at him strangely for a few seconds before getting on with their day.

The Doctor shook his head. He'd never understand Humans; they went through the same old routine every day, with almost no desire for the new and unknown. Perhaps that's why he preferred the company of people like June and Jack. They had jumped at the chance to travel with him, though June had been the responsible mother the entire time. If he was being honest with himself, having someone like June around really balanced out his own irresponsible tendencies.

"No, no," he muttered darkly to himself, "Remember, this was the last time. No more people lost. Today was to say goodbye."

So wrapped up in his thoughts, he almost missed the car that drove past him. It was purple-and-black and had a distinctive symbol, almost like a face on the back. It reminded the Doctor of the symbol on each Autobot, but more… evil.

"Well, at least it's something interesting," the Doctor said, and started following the car, which parked after a few minutes. Though the windows were tinted, the Doctor had a feeling that there was no one inside.

The Doctor circled the car several times, tapping his chin in thought. "Well, you're an odd model, aren't you? Let's see what makes you tick, eh?"

With a slight flourish, the Doctor pulled out his sonic screwdriver and pointed it at the driver's-side door. After a moment, the door opened and like the Doctor guessed, there was no one inside. It was with an excited smile on his face that the Doctor got in.

"Hello," he said, "I'm the Doctor. Take me to your leader."

**Cliffhanger! I'm evil!**

**So, this chapter really established certain events in Doctor Who: the Doctor met June and Jack sometime after 'The Poison Sky' and 'The Sontaran Strategem'. As for accidentally killing that first Sontaran… whoops. It happens. The rest of the Sontarans were going to blow up the planet. The Doctor has done worse to stop people.**

**I misspoke (mistyped?) in my Author's Note last chapter; I said that there would be no romance between the Doctor and June, and while that is true, I'm kind of pushing for June to have a crush on the Doctor, but nothing more serious will happen. I've noticed that the Tenth Doctor had quite a few people develop feelings for him. I'm just keeping him in character.**

**Next chapter, more questions will be asked, a few will have answers, and the Doctor annoys Megatron. **

**This muffin is bigger on the inside!**


	3. Meeting the Oncoming Storm

**DOCTOR WHO DOES NOT BELONG TO ME. TRANSFORMERS DOES NOT BELONG TO ME. HOWEVER, IT WOULD BE REALLY COOL TO HAVE A CAR THAT TURNED INTO A GIANT ROBOT WITH LASERS.**

**Yoda once said 'Size matters not', and that totally applies in this chapter. The Decepticons think that anything smaller than them (i.e., most organics) are barely worth the effort to step on them.**

**Obviously, they haven't met the Doctor… until now.**

Blue Box, Blue Bots

Chapter 3

Meeting the Oncoming Storm

**Jasper, Nevada**

Vehicon Drone 487 had a limited intelligence, at least by Cybertronian standards. To a Human, he was in a whole other league when it came to processing power, but to other Cybertronians, he was about as intelligent as the car he could transform into, albeit one with weapons.

Still, even the most brilliant of Decepticons would have been stumped at the strange creature that had just opened him up and sat in his driver's seat. The organic looked Human, but 487's scanners said otherwise; this person was practically radiating an unknown energy that made his processor hurt.

"Hello," the organic said cheerfully, "I'm the Doctor. Take me to your leader."

Something in his limited self-preservation routines predicted that declining this 'Doctor's' request would be very, very bad. At that point, 487 made quite the intelligent decision, for a Drone, anyway. He gunned his engine and sped off towards his pickup spot, the Doctor sitting comfortably in his seat.

"I don't suppose you have a radio, do you?" the Doctor asked, "I'd love some music right now."

Without waiting for an answer, the Time Lord took out the same device that had unlocked 487's door and pointed it at his radio. A tiny part of 487's processor wondered why he even _had _a radio; it wasn't like the Humans were going to look through his tinted windows, so why keep up that detailed a disguise?

A blue light shone from the silver tube in the Doctor's hand, and suddenly 487's radio began to play an old song.

"Oh, Elvis!" the Doctor exclaimed, clapping hands together once, "I remember going to his first live performance! He wasn't as good as this, of course, but oh, this takes me back!"

At that point, 487 tuned him out. Most of what the Doctor said made no sense, but if it did, 487 suspected that he'd get a splitting processor-ache. Instead, he sent a brief transmission to the Decepticon warship, the _Nemesis_, and to Soundwave, the master of communications and intelligence aboard the vessel. The message was simple: urgent pickup required, unknown being acquired, being has requested to meet with Lord Megatron.

As soon as 487 was outside Jasper, a greenish-white portal appeared in front of him.

"Oh, fascinating," the Doctor said, eying the groundbridge, "Some type of localized wormhole, right? This is getting exciting!"

Again, 487 ignored him, but the Doctor didn't seem to notice, choosing instead to go on and on about wormholes and space-time and other things that 487 simply wasn't programmed for.

…

**The **_**Nemesis**_

As the Doctor got out of the Vehicon—which transformed into a black-and-purple mech with small, clawed hands and a red V-shaped visor on its otherwise featureless faceplate—and looked around with undisguised wonder.

"Oh, wow, you've really got the efficiency down, don't you?" he asked, though not to anyone in particular, "I can definitely see you and the Cybermen getting along… actually, that would probably be a bad thing."

"Vehicon Drone 487!" a new voice barked, and a tall, yet incredibly thin Decepticon stalked into the large room. The Decepticon had forward-sweeping wings, enlarged shoulders, thin limbs, missiles on his arms, and hands that ended in long talons. His long legs ended in what looked like stiletto heels, though the Doctor didn't judge—he was sure that most of his Human friends would laugh, however. It was the Decepticon's optics that really caught the Doctor's attention, though; they were narrowed and suspicious, full of arrogance, deceit and cowardice. His posture suggested the same; he seemed to want to hunch over, but was forcing himself to walk forward with dignity.

"Sir!" Drone 487 saluted, a clear signal to the Doctor that this new Decepticon was someone of authority, but he suspected that this one wasn't in overall command.

"What is this lowly Human doing on this ship!?" the high-heeled Decepticon demanded, though he didn't notice the Doctor briefly scowl; sure, Humans had a lot of flaws, but that didn't mean that these living machines could look down on them.

Well, _physically_, they could look down on them, but that wasn't the point.

"Commander Starscream," Drone 487 began, "This creature isn't Human; I detected an unknown form of energy within him, and he used a technology not native to this world to override some of my noncritical systems."

The other Decepticon—now identified as Starscream—glanced down at the Doctor. "What exactly _are _you? You look Human to me."

The Doctor flashed a wide smile. "Hello, I'm the Doctor. I was hoping to speak to whoever is in charge here; is that you?"

He was fairly certain that Starscream was not, in fact, in charge, but it didn't hurt to double-check.

Starscream stood as straight as he could and seemed to puff out his chest. "I am Starscream, First Lieutenant of the Decepticons, servant to Lord Megatron."

"Oh, so you're _second_-highest on the totem pole," the Doctor scoffed, hoping to get a reaction out of the Decepticon, "And here I was hoping to speak to someone _important_."

Starscream's left optic twitched, as did his talons; he looked ready to eviscerate the Doctor, but restrained himself.

"You wish to speak to Lord Megatron?" Starscream sneered. "You should know that he will likely order me to crush you like the insect that you are."

The Doctor shrugged. "Maybe, but if I'm going to die, I'd at least like some questions answered."

Starscream shared a look with Drone 487 that essentially asked the same thing: was this organic insane?

"Well, if you truly do not care for your own life," Starscream said, turning on his heel and walking back the way he came, "Perhaps I can answer your questions; it would not do to burden Lord Megatron with such trivial concerns."

"Wonderful!" the Doctor beamed, then followed after the Cybertronian, though he had to jog to keep up. "Tell me, what was the original function of this ship?"

Starscream waved a talon at the walls idly. "It used to be a space station, capable of immense devastation, but Lord Megatron gave it sapience with Dark Energon. It gained the ability to transform, but it was a brutish thug of a Decepticon, called Trypticon. The Autobots critically damaged him in the final days of the war for Cybertron, so Lord Megatron repurposed him to become this ship, the _Nemesis_."

The Doctor frowned. "Is this Trypticon still alive?"

Starscream shrugged. "I do not know, nor do I care. He has fulfilled his purpose: to serve Megatron in any way possible, as must we all."

The Doctor was starting to see why the Autobots would have issues with the Decepticons. They had created a weapon, then gave it a soul, but when it became useless to them, they turned it into something else, without ever considering what it may have wanted. And the worst part of it all, the part that made the Doctor's blood boil, was that none of the Decepticons seemed to care.

It was at that moment that the Decepticons made the biggest mistake of their lives.

They'd made the Doctor angry.

Still, the Doctor wanted to know more. "So, why did you lot have a war with these Autobots?"

Starscream scoffed. "Lord Megatron desired to bring Cybertron back into a Golden Age; all that everyone else needed to do was bow before him. Those who did so were rewarded, but the fools who chose to resist plunged our world into a war that lasted for eons. Now, Cybertron is dead, and we must find enough Energon to start our race anew."

_In other words, _the Doctor mused, _the ones who didn't want to be ruled by a tyrant chose to fight. Did no one actually try talking things out? Primus would be ashamed; even he tried talking things out with Unicron once._

Starscream opened a door, which he and the Doctor walked through. The room they were now in was huge, by Human standards, at any rate. It was roughly ovoid, with a handful of Vehicon Drones manning several consoles; from the large console near the center of the room, the Doctor assumed that they were on the bridge.

Sitting on a massive throne, which rose above the rest of the room, sat an enormous Decepticon, even larger than Optimus, though not by much. He was covered in silver plating, with some purple splashed on his legs and the center of his chest, where the Decepticon symbol was placed. On his right arm was a massive cannon; the barrel was almost wide enough for the Doctor to step into! His helm vaguely reminded the Doctor of a bucket, though the face within the helm was filled with the promise of pain, destruction and hatred.

A small part of the Doctor's mind screamed at him to be careful around this one. The Doctor acknowledged that part of his mind for half a second, then ignored it.

"Hello," he said cheerfully, catching the giant Decepticon's attention, "I'm the Doctor. Are you this Megatron I've heard about?"

Megatron's purple optics narrowed at the Doctor for a moment, then focused on Starscream, who seemed to wilt under the stare.

"Starscream," Megatron said in a menacing, gravelly voice, "What is this creature, and why have you brought it to my ship?"

"L-Lord Megatron, I swear that I have just learned about it myself!" if it were at all possible, Starscream would have been sweating bullets. "He calls himself the Doctor, and he demanded to speak to you! From the scans that the Vehicon that delivered him here, he is not Human, though appearances say otherwise."

The Doctor looked up at the winged Decepticon with a raised eyebrow. "There's no need to be insulting; I don't call you effeminate because of your high heels, do I?"

For a moment, the Doctor wondered if he had been hanging around Humans for too long.

"They're support struts!" Starscream raged, momentarily forgetting about his fear of Megatron; apparently, that was a sore spot for him.

Megatron silenced the smaller Decepticon with a growl, then looked down at the Doctor. "You claim to be something other than Human? Your appearance says otherwise."

The Doctor grinned. "You're a race of giant robots who can transform into Human vehicles, and _you're_ lecturing _me _on appearances?"

Though the other Decepticons on the bridge were starting to pay more attention to the strange organic, it was at that point that the Doctor now had their undivided attention. This tiny creature dared to talk back to Megatron? No one was quite sure if the creature was brave, stupid or just crazy.

It appeared that today was a day for rare happenings, because instead of just blasting the Doctor, Megatron only leaned back in his throne and smiled.

"You make a valid point, Doctor," Megatron said, amused, "We Cybertronians aren't exactly ones to talk about appearances. So tell me, what are you, and why have you come before me?"

The Doctor tapped on his chin for a moment, as if thinking about it. "Well, I'm a Time Lord from the planet Gallifrey. I've got some questions about what you're doing on this planet, and if I don't like what I hear, I'm afraid that I'll have to destroy each and every one of you."

Once again, everyone stared; the Doctor showed none of the fear and awe that all organics seemed to feel when around their kind, and had just threatened to kill them all, even though he was surrounded on all sides, and within hostile territory.

Megatron, however, saw something else; there was something in the Doctor's tone, buried beneath the cheer, that reminded him of Optimus Prime. There was steely resolve, utter commitment to what he said; the Doctor clearly intended to destroy them, ludicrous as the idea was.

Deciding that today was far too unusual to pass up, Megatron humored the Doctor. "Very well, what are your questions?"

"Well, I've got a few," the Doctor said, briefly turning so that no one could see his hand dip into his coat and grab his sonic screwdriver. "First, how long have you lot been on Earth?"

"The Autobots have been here for three years," Megatron answered, "We have been here for slightly less time."

"So you followed them here, to finish your civil war?"

"We did not know that they were here until they sent out a signal," Megatron admitted, "However, we needed the Energon scattered across this world. The survival of our race depends on it."

"I'm sorry, did you say that the Autobots sent out a signal?" the Doctor was incredulous. "How did they do something so monumentally stupid?"

This time, Starscream answered. "Autobot codes are no match for our code-_breakers_."

"Well, that's something to be annoyed about," the Doctor said quietly, then looked Megatron in the optics. "One more question, then: where do the Humans factor into your plans?"

Megatron smiled again, but this time, there was no humor in it. "They will be honored to serve as our slaves… if they refuse, then we will kill them all."

At that, the Doctor's smile disappeared. "I see… well that settles that."

"What are you talking about?" Starscream snarled.

"I said that I'd destroy you if I didn't like what I heard," the Doctor said, slowly raising his sonic screwdriver for all to see. "Well, I didn't like what I heard."

Then the Doctor activated the sonic screwdriver, and all hell broke loose. Consoles flickered, alarms blared and systems randomly turned off and on. In all the confusion, no one noticed the Doctor slip out through the door he'd entered. When the chaos finally died down, Megatron searched for the Time Lord, but he was nowhere to be seen. However, there was still a ship-wide alert, informing the crew of system-failures everywhere at once.

"Find him!" Megatron roared, sending Starscream and a few Vehicons dashing from the bridge, "Find him and crush him!"

…

**Autobot Base**

"So, how can a box be a spaceship?" Miko asked, reaching out to touch the blue box's door, but Jack slapped her hand away. "Ouch! Dude, what did I do?"

"The Doctor doesn't like people touching the TARDIS," Jack explained.

"The what?" Miko raised an eyebrow.

"T-A-R-D-I-S," June said patiently, "It stands for Time And Relative Dimension In Space. And trust me, if the Doctor lets you inside, you'll know how it can be a spaceship… provided I don't kill him for taking my car!"

"How long is she going to be mad about that?" Raf whispered to Jack.

Jack shrugged. "The Doctor doesn't like people touching the TARDIS, Mom doesn't like people touching her car. Didn't you ever wonder why I never drove it?"

While Raf pondered that, the Autobots were working at the various computers on the base, trying to find the Doctor. They had been able to detect his energy for a short time, but then he had disappeared; the Autobots feared that he might have fallen into the hands of the Decepticons. Until they had information that said otherwise, they would focus on locating the _Nemesis_. However, most of the team only began working in earnest when Optimus practically demanded that they put their all into it.

Optimus' behavior over the last hour or so had been worrying, and not just to the Autobots; June had also noticed, and was becoming suspicious as to why.

Finally, she made her way over to the Prime and coughed loudly to get his attention. "Optimus, I think we need to talk for a minute."

Optimus looked down at the Human for a moment, then nodded. "I apologize, June, but this must be brief; our search for the Doctor is our top priority at the moment."

To Optimus' confusion, June actually laughed a little. "Don't worry about the Doctor, Optimus; he's faced worse than the Decepticons, trust me."

Optimus shook his helm. "I am sure that these Sontarans that you told us of were dangerous, but the Decepticons—"

June cut him off. "The Doctor has faced down things that would make Megatron looked like a drowned kitten. At worst, he'll need a new suit by the time he's done with the Decepticons."

Optimus blinked at the woman's utter conviction; when she spoke of the Doctor, there was a fire in her eyes that he rarely saw in any being. Saving June and her son would have undoubtedly fostered gratitude towards the Doctor, but what had he done to deserve such dedication? Optimus almost asked that question out loud, but wondered if June herself knew the answer.

"Optimus, I've got something!" Ratchet said loudly, catching everyone's attention.

"Have you located the Doctor?" Optimus asked.

Ratchet shook his helm. "I'm not sure about that so-called Time Lord, but I think I've just located the _Nemesis_. The ship's systems are going haywire, but I can't think of how or why—"

"It's the Doctor!" Jack said triumphantly, "No one messes with stuff better than him!"

"Regardless of the cause," Optimus said, heading for the groundbridge controls, "We cannot let an opportunity to deal a significant blow to the Decepticons pass us by. Autobots, prepare to roll out!"

"Optimus, wait!" June said, "If the Doctor is there—and honestly, I'd bet money that he is—I doubt he'll just trust you, especially since you guys tend to shoot things."

"What are you suggesting, June?" Arcee asked.

"Jack and I should go with you," June said, uncharacteristic eagerness in her eyes, "If anything, we might be able to keep him from getting mad at you."

"Why would he be mad at us?" Bulkhead scratched his helm, confused.

June and Jack looked at each other before June answered. "I think I know why, but I think that's something that the Doctor should answer."

Optimus looked at Arcee, Bulkhead and Bumblebee. "I do not wish to place any Humans in danger…"

"I'll take care of them, Optimus," Arcee volunteered, "Besides, the longer we talk about it, the sooner the 'Cons might fix their ship."

Optimus sighed. "Very well, but you must make sure that June and Jack are far away from the battle."

Jack grinned at his mother. "Just like old times, huh?"

June smiled back. "At least they're not Daleks, right?"

Jack shivered. "Don't remind me… ugh, I had nightmares for weeks after that."

Ratchet quickly activated the groundbridge, and the swirling portal appeared. "Good luck, all of you."

Optimus nodded, and he led the way into battle.

When they were gone, Raf turned back, but something caught his eye; or rather, the _lack _of something.

"Hey, the blue box is gone!"

Miko followed Raf's pointing finger. "Yeah, you're right! Um… where did it go?"

…

**The **_**Nemesis**_

As soon as the Autobots jumped out of the portal, they assumed combat positions. Optimus swept the area, his two large cannons searching for targets, but found none; the only sign of anything out of the ordinary were lights flickering erratically, and doors opening and closing at random intervals.

"Definitely the Doctor's work," June said from her position behind Arcee's leg.

"How can you tell?" Bulkhead asked.

"Look at everything," Jack was the one who answered, "On a scale of one to ten—one being not a problem at all, ten being you might want to get a new ship—how bad would you call all of this?"

Bulkhead looked around. "I don't know, a four, maybe?"

"Exactly," Jack hadn't stopped grinning. "If the Doctor wanted, he could have taken this ship apart, but since it hasn't exploded, he must want something. He's just messing with the 'Cons until he finds what he wants."

"And what does he want?" Arcee asked.

Both Jack and his mother shrugged. "No clue. We just know how he does things, but not why."

"If the Doctor is truly capable of destroying this ship," Optimus said severely, "We must move quickly. Bulkhead, you and Bumblebee head to the Energon storage room and have Ratchet open a groundbridge; move as much Energon as you can back to the base. Arcee, you and the Humans will locate the Doctor."

Bumblebee tilted his helm and beeped several times.

Optimus nodded. "You are correct, Bumblebee; I will take advantage of the confusion and take the battle to the Decepticons themselves. With luck, I may be able to locate and eliminate key Decepticon personnel."

The other Autobots nodded, their mission clear.

"Good luck, Optimus," Arcee said, then transformed into her vehicle-mode, allowing Jack to hop on, June sitting behind him. Arcee drove down the nearest hallway to begin the search for the Doctor.

Bumblebee and Bulkhead transformed next, a yellow-and-black muscle car and a green SUV respectively and drove towards the largest concentration of Energon on their scanners.

Optimus did not transform; instead, he jogged in opposite direction his team had gone, weapons ready.

The first Vehicons that Optimus met didn't stand a chance, terminated in seconds by Optimus' cannons. The next few barely lasted longer, but only because Optimus had switched from his ranged weapons to a long blade that sprouted from each arm. After a few swings, four Vehicons were reduced to three times as many pieces.

Optimus didn't let his easy victories make him overconfident, however; Vehicons were _meant _to be expendable. Once he met with a senior Decepticon, _then _he'd have a real fight.

…

"Any idea where he might be?" Arcee asked as she made a turn onto another hallway.

"Just look for the most amount of yelling," Jack suggested, shouting to be heard over Arcee's roaring engine, "It's probably the 'Cons getting really mad."

Sure enough, there was a loud roar of frustration just around the next corner. Arcee stopped to let the Humans get off of her, then transformed, her arm-blades at the ready.

"Stay here," she warned, then jumped out to confront whoever was there.

What she found, however, was surprising and a little sickening. Lying on the floor was Starscream, or at least, it looked like him if he was stuck halfway through transforming into his jet-mode. His arms were stuck to his sides, and his head was partially covered by the cockpit of his vehicle-mode; from the waist-down, he was still in his robot-mode, his legs scrabbling against the deck, but unable to lift his unbalanced body.

"Primus, what happened to him?" Arcee asked.

"Oh, that was me," a familiar voice said; Arcee looked up to see the Doctor standing on a Cybertronian-sized keyboard, studying the screen. "He was trying to stop me, so I hacked a few of his systems, then locked him down halfway through his transformation. Don't worry, he'll straighten himself out in a bit; I imagine it's like stretching out a cramp."

"You can do that?" Arcee was amazed; she'd never heard of anyone, not even the mad Decepticon scientist, Shockwave, who could do that to a Cybertronian so quickly.

The Doctor shrugged, not looking at her. "It wasn't too hard, really; you lot have no way to defend against hacking, did you know that?"

Arcee was torn between feeling insulted and a little bit afraid; Cybertronians had always prided themselves on their technological superiority, but this organic had just dismissed it like it was barely a footnote!

"Doctor, what are you looking at?" June asked as she and Jack came around the corner.

Finally, the Doctor turned around. "What are you two doing here? This is a dangerous place!"

Neither Darby said anything, only crossing their arms and shooting the Doctor a flat stare.

The Doctor sighed. "Right, this place isn't so bad, is it?"

"Not even up there on the top ten," Jack deadpanned, making Arcee look at him in astonishment; sure, Jack had taken meeting the Autobots fairly well, all things considered, but the adventures he'd had with them weren't that bad in comparison to his travels with the Doctor?

Just what had Jack and June been through?

"You didn't answer my question, Doctor," June pointed out, gesturing to the computer.

"Right, sorry," the Doctor tapped his chin as he studied the Cybertronian glyphs. "I'm looking through the historical databanks, specifically about the civil war on Cybertron. I'm trying to see what went wrong between the last time I was there and now."

"Find anything helpful?" Jack asked.

The Doctor shook his head. "No, most of the information was apparently lost over the eons, and a lot of the more recent data has been altered to suit the Decepticons' version of things."

"So it's useless?" Arcee looked disappointed.

"I didn't say that; it's certainly interesting."

Arcee wasn't sure whether to roll her optics or not, and she would never find out what she would have done, because a familiar chuckle echoed behind them all. It wasn't a laugh of amusement, but of sadistic pleasure and the promise of pain.

The three organics and one Cybertronian turned to see a Decepticon—a femme, just like Arcee—striding towards them. She was mostly humanoid, but had an insect-like abdomen, and four extra limbs sprouting from her back. Her optics were a solid purple, and narrowed at the sight of Arcee, while her mouth twisted into a sick smile.

"Oh, hello, Arcee," the Decepticon purred, her extra limbs twitching, "When the ship started going crazy, I hoped that you'd be here; now I can finish what I began on Cybertron."

"Airachnid," Arcee hissed, her servos transforming into a pair of Energon blasters, "About time you showed up. I've been meaning to offline you for a long time."

"Like you offlined poor Starscream?" Airachnid looked down at the Decepticon lieutenant, who chose that moment to start kicking again. "Oh, he's _not _offline… let me fix that."

With a swift stab, Airachnid drove one of her extra limbs through Starscream's spark chamber, killing him instantly. To the horror and disgust of the others, she removed the appendage and licked off the Energon that was smeared across it.

"Why would you do that!?" the Doctor demanded, "Wasn't he one of your own!?"

Airachnid shrugged. "It's not like we're friends; it's every Decepticon for themselves, really."

The Doctor scowled and dropped down to the floor. June and Jack saw the look on the Time Lord's face and wisely backed away, but Arcee and Airachnid were respectively confused and amused.

"What are you going to do, little man?" Airachnid smirked as another of her extra limbs shot forward, ready to impale the Doctor.

The only thing that moved was the Doctor's arm, which raised the sonic screwdriver and pointed it at the oncoming limb. There was a hum from the device, and then a screech as the leg locked up, then abruptly fell to the floor.

Airachnid's optics went wide, then returned to their normal expression when the frozen limb began working again.

"What was that?" she asked.

"A taste," the Doctor said in a low, dangerous tone that made even Airachnid pause, "A taste of what I can do to you. I could shut you down, or lock up every part of you save for your optics and let you watch the world pass you by, or I could force you to rip yourself apart."

Airachnid prided herself on being good at reading most beings; after torturing so many Autobots on Cybertron during the war, she knew when a prisoner was going to break, or when they were going to keep fighting. The Doctor wasn't just going to keep fighting… he was going to _win_. The sort of fire in his eyes was that of someone filled with a righteous fury and the power to back it up.

"How does it feel?" the Doctor asked, stepping forward, "To be on the other side of things, I mean. How does it feel to not be in control, to have someone else hold all the cards? Oh, I know who you are, I read your file; you've tortured and killed thousands, not for a grand purpose, but because you wanted to. Monsters like you are why I do what I do.

"I'm the Doctor… and I am going to stop you."

Airachnid took a step back… or tried to, at least. Her legs refused to move! It wasn't fear that was holding her in place—a quick diagnostic proved that her legs were literally locked!

The Doctor held up his sonic screwdriver and waved it tauntingly. "You should really know something about me: never let me talk, because I'm probably doing something you don't want me to."

"Thanks, Doctor," Arcee said grimly, aiming her blasters at Airachnid, "Time to finish this."

"Wait, no—" the Doctor's protest was cut off by the sound of Arcee's weapons, which drove two small holes through Airachnid's chassis; one through her helm and the other through her spark. The Decepticon femme fell to the floor, dead.

Arcee's blasters shifted back into servos. "That was for you, Tailgate."

"I didn't want to execute her!" the Doctor shouted, "I wanted information, and I wasn't just going to kill her like she killed Starscream!"

"Why not?" Arcee asked.

The Doctor sighed and ran a hand over his face. "Because that makes us just as bad as her."

Arcee remembered Optimus telling her something similar after she had encountered Airachnid on Earth. Deep down, she knew that revenge wouldn't really bring her satisfaction, but she'd done it anyway. It was no wonder that she felt empty inside.

June walked over to the Doctor and tentatively held his hand in hers. "Doctor, it's okay; you didn't pull the trigger, Arcee did. Come on, we need to keep moving."

The Doctor smiled at her. "Thank you, June, you're right. Come on, let's see what else we need to do."

Arcee glanced away from the disapproving look coming from Jack, telling herself that it was because she needed to update the other Autobots.

"Arcee here; Starscream and Airachnid are both neutralized."

"_Understood, Arcee," _Optimus replied, _"Bulkhead and Bumblebee have retrieved a large portion of Energon, and I have engaged Breakdown and Knockout. Have you found the Doctor?"_

"Yes, and he's unharmed."

"_Good. Return to base immediately; the rest of us will do the same as soon as we can."_

"Yes, sir," Arcee cut off communications and looked down at the three organics. "I don't think I can carry three people in vehicle-mode; looks like we're heading back to the groundbridge point the slow way."

"I hate the slow way," the Doctor said, a smile on his face as he pointed to something behind Arcee, "Why don't we take _my _way?"

Arcee turned and, to her shock, the Doctor's blue box was right behind her! "What… how…?"

"Wouldn't be the first time she's done that," the Doctor said, running over the box and pulling out a key; once the door was unlocked, he waved at all of them. "Well, come on, don't just stand there!"

The Doctor ran into the box, June right behind him. Arcee was still confused, unsure of what to do, until Jack tapped on her leg.

"You might want to transform," he said, "You won't fit through the door otherwise."

"But it's a box…" Arcee began to say.

Jack shook his head. "Just trust me on this."

Once the teen had disappeared into the box, Arcee shrugged, then transformed and drove into the box, but slowly, so as not to hit the Humans or Time Lord. However, once she was inside…

"What the…!?" Arcee didn't transform, but from the way she sounded, she would have looked completely gobsmacked.

The inside of the box, the TARDIS, was huge! It was a large, circular room with supports that almost seemed organic. The center of the room was dominated by a raised, circular platform that had a transparent tube running from the ceiling down to what looked like a control panel built around it. There were buttons and switches arranged almost haphazardly, as if it were built by a lunatic.

"Welcome to the TARDIS," the Doctor said, smiling as he leaned against a railing, "Something you want to say?"

"It's… it's bigger on the inside!" Arcee's processor ached trying to understand what she was seeing. Just past the platform, she spotted an open door that apparently went even further; how big was this box!?

"Oh, it is?" the Doctor looked around, as if noticing for the first time, but inside, he was almost cackling with glee; he loved the reactions that people had when they entered the TARDIS for the first time.

"Wait, where are Jack and June?" Arcee asked.

"Right here!" June called out, as she and Jack entered from the other door; both were carrying bags. "I knew we left some clothes here!"

"You didn't need to bring any!" the Doctor said, rolling his eyes, "I have an entire wardrobe!"

From the expression on Jack's face, this was an argument that his mother and the Doctor had had before.

"Um, what happens now?" Arcee asked.

"Well, we really need to leave," the Doctor said, moving over the console and began flipping switches and pushing buttons, almost at random.

"We're going back to the base, right?"

"Nope!" the Doctor replied cheerfully, "We're going to Cybertron, shortly after I met Primus the first time around."

"But I thought you said that you couldn't do that?" June asked.

"Well, kind of," the Doctor admitted, "I've got a way around that, I think. It's all wibbly-wobbly, timey-wimey."

"And if it doesn't work?" Arcee asked, then looked at the Humans. Jack looked excited, practically bouncing up and down at the thought of traveling with the Doctor again. June was more composed, but still had a wide grin on her face.

The Doctor shrugged. "We could die, I suppose."

Before Arcee could protest, the Doctor flipped one last lever. "Allons-y!"

The TARDIS began to make the same groaning, wheezing sound as before the entire ship began to shake. The Doctor, June and Jack braced themselves, the Time Lord grinning from ear to ear.

_Primus help me, _Arcee thought, _I think I've just been kidnapped by a lunatic!_

**So there's the next chapter, folks! Sorry that it wasn't as long as the last one, but I promise that the next chapter will make up for it. Now, odds are that one of two things will happen: either I will make one really long chapter wrapping up the conflict between the Autobots and Decepticons, and then a really short epilogue chapter, or I will write two medium-sized chapters wrapping up the conflict and then short epilogue. I'm fine with either, but if I do the second one, you might be annoyed by the cliffhanger. **

**Also, yeah… I killed Starscream and Airachnid. Starscream was OK in 'Transformers Prime', but Airachnid annoyed the hell out of me. I'm sorry that I didn't put a lot of Transformers action into this, but this story is more Doctor-centric than anything else. **

**Next chapter: The Doctor speaks to Primus, and Arcee learns why the Doctor is the Last of the Time Lords.**

**The Cybermen are superior in only one aspect.**

**What is that?**

**The Cybermen are better at making muffins.**


	4. Peace in Our Time

**DOCTOR WHO DOES NOT BELONG TO ME. TRANSFORMERS DOES NOT BELONG TO ME. MY REPLICA SONIC SCREWDRIVER BELONGS TO ME, AND I SOMETIMES POINT IT AT AUTOMATED DOORS WHEN THEY OPEN TO MESS WITH PEOPLE.**

**You know, it's a little strange that I wrote this story with the Tenth Doctor, even though the Eleventh is my favorite. I guess it's just because I wanted to work in June and Jack without them clashing with Amy and Rory.**

Blue Box, Blue Bots

Chapter 4

Peace in Our Time

**The TARDIS**

Arcee had never liked traveling inside of vehicles. Maybe that was because she could already become a vehicle, or maybe it was because she didn't like putting her life in the control of something else. Whatever the cause of it, Arcee was the only passenger in the blue box that was _not _having a good time. The Doctor, June and Jack, on the other hand, were laughing like lunatics, as if the bucking, jumping vessel that felt like it was about to crash and burn was an enjoyable walk through the park.

Then again, from the way the Darby family had talked about the Doctor, maybe this sort of thing _was _fun. Either way, it was certainly making her reevaluate the two Humans' personalities.

"Hold on!" the Doctor said, grinning madly as he ran around the TARDIS's controls, flipping switches and hitting buttons, "This is where things get a little bumpy!"

"I thought things were _already _bumpy!?" Arcee asked incredulously.

"No, this is just how the TARDIS normally is," Jack said in between laughs, "When things get bumpy… well, I don't think your kickstand is going to cut it."

Nervously, Arcee wheeled herself over to where the stairs were close to one of the room's coral-like supports and wedged herself there. To make things even more concerning, neither Jack nor June followed her lead, or Jack's own advice; instead, they only tightened their hold on the TARDIS's controls, only leaning out of the way when the Doctor needed to fiddle with something that they stood in front of.

Arcee found that her decision to secure herself was a good one, because the turbulence that rocked the blue box now made what happened before seem like a light shake. Lights blew out, sparks flew from panels, and the glowing light at the center of it all flickered and groaned in protest.

"Don't worry, girl!" the Doctor shouted, patting a panel with what Arcee could only describe as loving concern, "Just a few more seconds!"

Finally, much to Arcee's relief, the shaking stopped; the only problem was that it stopped so suddenly that she was jerked out of her secured position and flung across the room, where she slid to a halt by the door.

"Ouch…" she muttered painfully, but neither the Humans nor the Time Lord seemed hurt; if anything, they were laughing even more, even if they were sprawled on the floor.

"Oh, I've missed that," June said, wiping a tear from her eye as she accepted the Doctor's hand to help her up, "How's the TARDIS doing?"

The Doctor grinned—not his usual, manic grin, but an almost tender smile—at June's question. Unlike most people he'd traveled with, June treated the TARDIS like a living thing, which she was, and showed real concern if the ship/time-machine was damaged. Jack had picked up on that soon after his mother did, but it was June who had truly earned his respect for what she did.

"She's fine," the Doctor said, after he checked a few instruments, "Self-repairs are already underway. She's tough, though; we'll be able to fly out of here either way. That's good, normally we'd get stranded for a while or something."

Arcee felt her spark skip a beat; this maniac could have stranded them… wherever they'd gone!? She looked at the Darby's, who were no longer smiling, but instead giving the Doctor a flat stare. Apparently, they weren't happy with the Doctor's announcement, but looked used to it. Arcee swore that she would get the whole story out of one of the Humans as soon as this was over.

"So," Jack said, walking over to Arcee and setting her upright, "Did we make it to Cybertron?"

The Doctor tapped at a few more buttons before looking at a screen. "Yep. Turns out that we've landed shortly after the last time I was here."

"But wait," June said, frowning, "I thought you said that Primus time-locked the whole planet, so how did we get here?"

The Doctor looked a bit smug, a sign to the Humans that he was about to explain how he was cleverer than someone else.

"Well, despite being incredibly powerful and intelligent, Primus has a rather linear approach to time-travel," the Doctor said, "He put up something like a barrier up around the planet to keep me out. However, he only time-locked the planet a few weeks from now; the rest of the barrier, which he put up right after I left, is just to keep the TARDIS from landing, but come on, I've gotten around Dalek defenses before, and Primus is an even bigger novice than them."

Arcee felt a little offended at how the Doctor was belittling her people's creator, but Jack raised his hand before she could say anything.

"Wait, so it's not that you got around the time-lock," he said thoughtfully, "It's that Primus made a mistake?"

"Exactly," the Doctor said, snagging an object from a small compartment before walking over to the door. "Who's up to see Cybertron?"

"Hold on," Arcee said, "Cybertron doesn't have an atmosphere capable of supporting Humans; if Jack and June go out there, they'll die!"

The Doctor scoffed. "Oh, don't worry, I've extended the TARDIS's environment so that that we'll be able to breathe. Just… don't go too far."

"How far is too far?" June asked, knowing how the Doctor liked to be vague.

"If I stop walking, do not go past me," the Time Lord said, his face now stern, "In fact, you two should stay behind me at all times."

"Got it," Jack said with a confidence Arcee had seen more of in the last day than in the past few months she'd known him; had he been able to fool her for that long?

"Don't worry, Doctor," June smiled, "We _have _done this before."

The Doctor smiled back, then opened the door.

…

**Cybertron**

As soon as she rolled out of the TARDIS, Arcee transformed and gasped. The last time she had been to her homeworld, it had been nothing but rusty ruins and bad memories. Now, the planet was pristine, in an empty, primal way. This was a Cybertron that had known conflict, but of a primal, life-giving kind, not one that had left it as an empty husk.

Jack noticed a tear of Energon slide from one of Arcee's optics. "You okay, Arcee?"

The Autobot quickly wiped the tear away. "I'm fine, Jack, it's just… I never thought I'd see my home again."

There was a comforting pat on her leg, but it didn't come from Jack, or even June—rather, it came from the Doctor, who gave her a sympathetic smile.

"I know how that feels."

Before Arcee could ask what he meant—it obviously had something to do with why he called himself the Last Time Lord, but with all that had happened, she hadn't had a chance to ask—the Doctor pulled out his sonic screwdriver and began fiddling with it.

"What are you doing?" Jack asked.

"Well, I'm not sure where exactly Primus and the Thirteen Primes are," the Doctor said, holding the screwdriver as high as he could, "So I'm sending a signal. This might be a bit… loud… Arcee, fair warning."

The warning was not, in fact, very fair, because as soon as the Doctor activated the screwdriver, Arcee clutched her audio-receptors as agonizing sonic white-noise was driven into her helm. The noise was so painful that it drove her to her knees, but thankfully, the sound was gone almost as soon as it began.

"Sorry about that," the Doctor said, "Like I said, I don't know where Primus or the Thirteen are, so I needed the signal to be strong enough to be detected all over the planet."

"Fine," Arcee grunted as she got back up, "just don't do it again."

Jack looked around at the smooth, interlocking plates of metal that was Cybertron's surface for several seconds, then turned to the Doctor.

"Um, what happens now?"

The Doctor sighed. "Now we wait… I hate waiting."

…

The wait only turned out to be a few minutes long, something that June was grateful for. As much as she adored the Doctor, seeing him pace a circle around the TARDIS was not something she wanted to spend her time wasting on.

Jack kept himself occupied by asking Arcee about the various constellations that dotted the Cybertronian night sky. He knew that constellations were arbitrary, his travels with the Doctor had taught him that, but it was better than doing nothing, and it kept Arcee occupied as well.

Finally, the wait was over when the ground began to shake. It wasn't the shaking that would come from an earthquake, but rather like shaking that came from the footsteps of giant alien robots. The only difference this time was that these were much, much bigger footsteps.

Over the horizon, a massive being walked towards them. It was Cybertronian, that much was obvious, but he was _huge_. Even at his tallest, Optimus wouldn't have been able to see over Primus' foot. Speaking of the Last Prime, the creator of all Cybertronians kind of looked like him; his armor resembled that of a medieval knight, though the plates of his chassis looked more like stone than metal. Arcee could see several irregularities in Primus that would have never existed in any current Autobot or Decepticon. Still, Primus exuded confidence, the kind that could inspire troops to charge into certain death with only a word or a look.

Arcee found herself torn between standing tall or kneeling in reverence. Before she could make a decision, however, Primus himself knelt, though only because he wanted to inspect the organics and the future-Cybertronian.

"**Doctor," **Primus boomed, narrowing one massive blue optic at the Time Lord, **"You have regenerated. I have not seen this face before."**

"Yeah, I've changed quite a bit since we last spoke," the Doctor said calmly, "About a century for me. Say, where are the Thirteen? I thought they'd be here with you."

"**The Thirteen Primes are tending the Well of All Sparks, preparing to welcome the next generation of my children." **Primus' voice turned stern. **"You are forbidden from setting foot on Cybertron, Doctor."**

"Since when has being told not to go somewhere ever stopped me?" the Doctor replied cheekily.

Arcee had never thought a being of such power and majesty as Primus could scoff, but he clearly did so. He then turned his attention to her, and Arcee found herself trembling; Primus, creator of her people, was paying attention to _her_!

"**Who is this, Doctor?" **Primus asked, **"This femme is Cybertronian, but she is so… different."**

"M-My name is Arcee, L-Lord Primus," Arcee managed to say, "It's an honor to meet you in person."

"She's from a few hundred million years in the future," the Doctor cut in, raising an eyebrow at Arcee's behavior, "Did you know that by that time, this world will have been so ravaged by war that the two sides of said war will abandon it, taking their battle to other worlds?"

Primus paused for a moment, then looked at Arcee. **"Is this true, child? Have all Cybertronians begun waging war on other worlds?"**

"Y-Yes, Lord Primus," Arcee said, "My side, the Autobots, is led by Optimus Prime, and we've been fighting against the Decepticons, led by Megatron."

"**And you, Doctor—were you aware of this conflict? Is this war somehow your doing?"**

The Doctor held up his hands in protest. "I just found out about this today! I'm trying to stop it!"

Primus' optics narrowed dangerously. **"When you are involved, Doctor, whole worlds are threatened. Has the Time War taught you nothing?"**

Now it was the Doctor's turn to give a glare. "The Time War taught me much, Primus. I have spent every day since then trying to save lives, to make up for what I've done!"

Arcee looked down at Jack and June. "Time War? What are they talking about?"

As soon as Primus had mentioned the Time War, the blood had drained for June's face. There were few things that the Doctor told one Darby and not the other, but June had sworn to never tell Jack the few details she'd learned. She decided to give the basic version, the one that Jack knew.

"There was a war between the Doctor's people, the Time Lords, and the Daleks—they make the Decepticons look like saints. The Time War was so bad that the universe was burning at every point in history. The Doctor… ended it."

Primus sneered. **"And did the Doctor tell you **_**how **_**he ended the Time War, organic? Did he tell you of the sin he bears?"**

"I did," the Doctor said, his face filled with regret, but he stood tall as he turned to Arcee. "As the war went on, things got… well, 'bad' doesn't begin to describe it. Whole species were erased from history, while nightmares that should never have been born walked across innocent worlds. My people were supposed to be the heroes, while the Daleks were the monsters. At the end, though, I looked at both sides… and I couldn't see a difference.

"And so I ended it. I destroyed them all—Dalek and Time Lord alike. In the name of peace and sanity, I committed genocide."

Arcee was dumbstruck; she'd thought that the Doctor was a brilliant, possibly crazy, alien who seemed more concerned with having fun than doing anything responsible. Now here he was, telling her that he'd wiped out two entire species… and one of them was his own.

Both Jack and June had heard this before—June was just thankful that the Doctor had skipped over some of the more gruesome details, which still sometimes gave her nightmares—but it was no less heartbreaking. The Doctor was a man who had sacrificed everything he'd loved in order to save the universe, leaving him full of regrets, and so, so alone.

"That's why I came to Cybertron after the war ended," the Doctor continued, "I know how powerful Primus is, and I wanted to warn him about not following the path of the Daleks or the Time Lords."

"**And my people shall not," **Primus boomed, **"I shall set down laws that ensure that no Cybertronian interferes with the flow of time."**

"Not good enough," the Doctor said, folding his arms, "Your people brought their war to a planet full of innocent beings. Under the articles of the Shadow Proclamation, your people are committing acts that will see them hunted down. You have to send a message to them, telling them to abandon this war and return to Cybertron with peaceful intentions."

Primus' was frozen for a moment, before he turned to Arcee. **"You, child—tell me of the world your war has traveled to."**

Arcee was a little surprised by the request, but she complied. "Well, it's a very small planet, called Earth by the Humans—like Jack and June here," the two Humans waved cautiously at Primus, who barely looked at them, "The planet has a lot of Energon, which is why we're there; Cybertron no longer produces it."

Primus nodded. **"Has this world suffered because of your presence?"**

Arcee hesitated. "Um… I know that the Autobots haven't attacked any Humans besides MECH—"

"Who?" the Doctor asked.

"A bunch of people who want to capture any Cybertronian they can, then dissect them and use their technology for their own gains," Jack informed him quietly.

The Doctor nodded. "Note to self: do something about MECH."

"—but we've managed to keep the Decepticons from doing too much damage," Arcee went on, "As far as I know, Human casualties have been extremely light."

The Doctor scowled. "There shouldn't be _any _casualties; your people shouldn't have even left your own system. We agreed on that, Primus!"

"**Indeed, we agreed that no Cybertronian should venture beyond this system," **Primus said, **"But is it not the right of all intelligent beings to follow their own desires?"**

"You told me that your people would never threaten another species unless it was in self-defense!" the Doctor shouted, "Humanity is far too primitive to be a threat to your people, and even these MECH people only attacked because Cybertronians resumed their war on Earth!"

"**You dare lecture me!?" **Primus stood up to his full height, glaring down imperiously, **"I am Primus, embodiment of order!"**

"Yeah?" the Doctor smiled, but there was little humor in it, "I'm the Doctor; I think I win."

Primus scowled. **"Once again, Doctor, you prove why organics can never be trusted."**

The Doctor blinked. "Excuse me?"

"**The Time War was caused by organics, as is every conflict and unnatural disaster that takes lives. It is no wonder I permitted a war between Cybertronians to take place and spread to other worlds; the organics must be erased or enslaved, for their own protection, and that of my people."**

Arcee was shocked by Primus' words, but the first thing she thought to ask was, "You 'permitted' a war to take place? How could you permit anything? You became Cybertron's core!"

"He's a being of near-limitless power," the Doctor said, the first one to figure it out, "He had to have been aware of what was happening and more than capable of stopping it. He could have ensured your society stay on the right path with just a word, but he let it fester and stagnate until a war started."

"**You are correct, Doctor," **Primus said, **"Since you visited me, I have been planning on how to ensure my peoples' survival from the mistakes of organics."**

"But…" Arcee started shaking, but if it was from disbelief or anger was uncertain, "But if that's true, you let millions—no, _billions _of Cybertronians die, all so that we could spread our war to other worlds?"

"He probably helped speed things along," the Doctor mused, "When Primus explained his rules for Cybertronian society, the Primes would have direct contact with him. I'm betting that he knew things would go wrong if he cut off contact, so after a few generations, that's what he did."

"**You should be proud, Doctor," **Primus boomed, **"Without you, I would never have realized the threats the organics posed. For saving my people, I thank you."**

"Not all organics are evil!" the Doctor shouted, "In fact, most of them are the exact opposite of evil! Look at the Humans here: they're a young species, prone to violence and unbelievable stupidity—"

"Hey!" Jack said indignantly, but was quickly shushed by his mother.

"But that's because they have so much to learn!" the Doctor continued, "Once they do, they'll be so much greater. I've seen what they can become, Primus: in the heart of every Human lies the capacity for compassion, bravery and love, the kinds of virtues that you championed! How can you wipe them out with that knowledge?"

Primus crossed his massive arms. **"Because of you, Doctor. You fail to grasp that every world you visit suffers misfortune and calamity; the destruction my Cybertronians will unleash is a far cry from what you have done. You are the Oncoming Storm, the destroyer of worlds; what right have you to call me into question?"**

The Doctor took a deep breath before giving Primus what June called The Look. She had only seen it once, during an encounter with the Daleks; with just that look, those Daleks ran for their lives, an image June would remember until the day she died. The Look was a reminder that anyone who received it was beyond the Doctor's forgiveness; he wouldn't just defeat them, he would _destroy _them.

"I'll tell you why I have the right," the Doctor said, so softly that it was a wonder that Primus even heard him, "I have the right because, unlike you, I _regret _what I've done. I regret wiping out my people, and I mourn for every life I've had to take and every friend I've ever lost. You, however… you have none of that.

"Cybertronians built you up as a benevolent god, but you're no better than Unicron! No, scratch that, you're even _worse_—at least Unicron was honest about what he was, but you hide behind your twisted morals of maintaining order and saving your own people! Well, I have news for you: letting billions of your people die in a pointless war, just so that they can make others across the universe miserable _isn't saving them_!"

Throughout the Doctor's rant, Primus had gone from irritated, to angry, to furious, and finally, to royally pissed off. His optics blazed to the point that they were no longer blue, but white, like a supernova.

"**Insolent organic!" **he roared, raising a fist to smash the Time Lord, **"You will not see another life! I will crush you until you run out of faces!"**

Before Primus had even finished speaking, the Doctor had grabbed Jack and June, practically carrying them back to the TARDIS.

"Get in, get in!" he shouted, then looked at Arcee. "Well, are you coming or not!?"

Arcee hesitated for just a moment, a moment that the Doctor used to get inside the TARDIS, then transformed and sped into the time machine. The doors had barely closed behind her when she heard the now-familiar wheeze-groan of the TARDIS preparing to leave.

"Hold on!" the Doctor shouted, "Gonna have to make a couple trips!"

Being so large, Primus was very, very slow. By the time he'd taken the one step necessary to reach the TARDIS and attack it, the blue box had disappeared. Primus scowled.

"**He has fled," **he said a moment later, then turned to the small being who had been hiding in the shadows on his shoulder, **"I did not enjoy that. I respect the Doctor, and I do not wish for his destruction."**

"But you care more for your people than for him, correct?" an arrogant, British voice asked, "I need the Doctor broken, Primus; I want all of his accomplishments to fall apart before I come for him."

Primus sighed. **"Is this task finished? May I return to my own labors?"**

"Of course," the Master said, smiling behind his spacesuit, "Consider our little agreement fulfilled."

…

**The TARDIS**

After the escape from Cybertron, the Doctor had landed the TARDIS and retreated to a small corner of the control-room. He sat on a chair and brooded, his chin resting on one fist, while his other hand was in a pocket of his coat.

Arcee wasn't doing so well either. She was leaning against the wall near the door, occasionally twitching in her vehicle-mode.

With both aliens lost in unpleasant thoughts, the Darby family split tasks.

"I'll handle Arcee," Jack offered.

"Yeah, you get the easy job," June half-joked, "I have to deal with a brooding Doctor."

Jack smiled, but there was no humor in it. He and June had seen this sort of thing more than once in their travels with the Doctor; while most were exciting and fun, there had been times that the Doctor had been confronted with something from his past, usually having to do with the Time War. Afterwards, he had become cold, distant, and more than a little angry.

"Hey, partner," Jack said, sitting down next to the motorcycle, "Not the best day, right?"

Arcee froze. "Jack, I just found out that the entire reason for the war on Cybertron was because your 'friend' scared Primus so much that he was willing to let most of us die. This is worse than losing Tailgate and Cliffjumper all over again."

Jack winced; Arcee rarely mentioned her previous partners, both dead now, and she'd never mentioned both in the same sentence.

"The Doctor… isn't perfect," Jack admitted, but still tried to defend his friend. "He's made mistakes, and people have died from some of those mistakes. The one thing I know about him, though, is that even if it hurts, he'll keep getting back up; the losses drive him to do more good. It might be hard to believe, but for every life lost on his watch, he saves a city, a species, an entire planet."

"That's not as helpful as you might think," Arcee said sadly, "So many of my people have died…"

Jack gently placed a hand on Arcee's gas tank. "I'm not trying to be helpful. I'm just telling the truth. Sometimes… sometimes, there aren't any happy endings; you just have to do the best you can."

Arcee didn't reply to that, and Jack didn't press further; instead, the Human gently leaned against the Cybertronian, giving her comfort with his presence.

June, meanwhile, cautiously approached the Doctor. She knew he would never hurt her, or even raise his voice to her in a threatening manner, but she still didn't want to set him off.

"Doctor," she said gently, sitting next to him, "are you going to be okay?"

"One hundred years," the Doctor muttered, half to June, half to himself, "That's how long the Time War has been over for me, and even now, it's still hurting people."

June shook her head. "Doctor, you couldn't have known that this would happen."

"But I should have," the Doctor argued, "June, Primus was alive during the Time War, but he remained neutral. I warned him about messing with time, but he wouldn't even consider it if I didn't tell him what I did. What _I _did pushed him to want to eliminate organics; how many people on how many worlds have suffered because of my mistake?"

"I don't know," June admitted, "But if you hadn't told Primus, he might have messed with time-travel, right? Think how many more people might have suffered if Primus decided to get involved personally."

The Doctor didn't reply, but June had thought that might happen; despite all that she'd learned with traveling with him, the Time Lord had almost nine hundred years more experience than her.

"Wait a second," Arcee said from across the room, catching everyone's attention, "This is a _time machine_!"

"You're figuring this out now?" the Doctor snapped.

"No, I mean we can stop all of this before it ever begins!" Arcee said excitedly, "We can travel to before you met Primus and tell your younger self not to interfere!"

The Doctor sighed. "That won't work. I can't interfere with my own personal history. Besides, I now know what happened after I visited the first time; these events are now locked, and cannot be changed."

"But—" Arcee began to protest, but it was Jack who stopped her.

"Arcee, time-travel isn't magic, there are rules… some that even the Doctor can't break."

Despite being a motorcycle, Arcee seemed to slump. "So it's pointless? All those lives lost… and there's nothing we can do?"

The Doctor took a deep breath, then gave a small smile. "Well, there is _one _thing…"

Two Humans and a motorcycle turned to face the Time Lord as he pulled a small, rectangular device from his pocket.

"How mad do you think Megatron would be if he found out that he'd been manipulated since before he rose to power?"

If Arcee was in her robot-mode, she would have blinked, then smiled. "He'd probably end his war just to spite Primus."

"And I'll bet that Optimus would jump at the chance for peace," Jack added, "But how are you going to convince Megatron that Primus was playing everyone?"

The Doctor's smile grew devious as he waved the device in his hand.

June's eyes went wide, before a similar smile appeared on her face. "Oh, Doctor, that is brilliant!"

…

**The **_**Nemesis**_

Megatron scowled as the injured, but still functional, forms of Knockout and Breakdown landed in a heap at his feet. Just down the corridor, Optimus Prime's swords turned back into servos as he calmly approached Megatron.

"Your best fighters are dead, unable to help you…" Optimus noted that Soundwave, who had been right behind Megatron, had taken a step back, "or are abandoning you. Now it's just you and me, Megatron."

Megatron snarled and raised his right arm, aiming his massive cannon at Optimus. "No, it's just me, Prime!"

Optimus' servos turned into a pair of blasters and aimed them at his nemesis. "One shall stand…"

"And one shall—" Megatron began to finish their age-old pre-battle phrase, when he was interrupted by a groaning, wheezing noise nearby. Both he and Optimus looked down to see the TARDIS—though only Optimus actually knew what it was—appear between them.

The doors opened, releasing the Doctor, June, Jack and Arcee. The Autobot quickly transformed, but uncharacteristically, she didn't aim her weapons at Megatron; in fact, she seemed to barely acknowledge the Decepticon's presence.

"Arcee, step back," Optimus ordered, "It is time to end this."

"Oh, you're right about that," the Doctor said with a glare, "It's time for this war to end."

"You!" Megatron's optics blazed with fury as he shifted his aim towards the Time Lord. "You are responsible for all of this!"

The Doctor met Megatron's cannon with his sonic screwdriver. "More than you know."

The screwdriver hummed for a moment, and then Megatron's arm fell limply to his side. Before anyone else could say or do anything, the Doctor turned to Optimus and deactivated both of his arms.

"Now that I know you two won't try anything," the Doctor said in a low voice that chilled both Megatron and Optimus down to their sparks, "You're both going to stop trying to kill each other and listen to me.

"Arcee, give this to someone with computer skills," the Doctor continued, handing a small device to the Autobot femme.

Arcee gave a weak smile. "That shouldn't be too hard."

She walked past Megatron and up to Soundwave, holding out the device; the Decepticon took another step back, not wanting anything to do with anything from the Doctor.

"Oh, don't be such a baby," Arcee said irritably, "It's just a message from Primus, something that everyone needs to hear."

For those who didn't know what Arcee had just been through, it wasn't sure what was more surprising: that Arcee had announced that she had a message from Primus so casually, or that she had said the name with such venom in her voice.

Soundwave gingerly took the device from Arcee's servos, but didn't move from his spot, choosing instead to look at Megatron. The Decepticon leader thought about it for a moment; the Doctor had easily disabled both him and Optimus, and it didn't seem impossible for him to destroy them both if he wanted to. No, the Doctor wanted this message broadcast to everyone on the _Nemesis_, and he wanted the two leaders alive to hear it.

"Do it, Soundwave," Megatron said quietly.

The silent Decepticon nodded and left for the bridge. Once he was gone, the Doctor looked from Optimus to Megatron.

"If I free you, will you promise not to kill each other?"

Something told both leaders not to lie to the organic, and they nodded. The corner of the Doctor's mouth lifted as he pointed his screwdriver at them again. After a moment, both could move, but they did not attack each other; instead, all of them waited patiently for Soundwave to play the message.

Well, the Doctor didn't wait patiently; he spent some time fixing both Breakdown and Knockout, and the two Decepticons were soon conscious. They looked first at the Autobots and organics, and then at Megatron, who only shook his helm at them.

Finally, a deep, regal voice began speaking, reaching every corner of the ship.

"_**It is no wonder I permitted a war between Cybertronians to take place and spread to other worlds; the organics must be erased or enslaved, for their own protection, and that of my people…"**_

…

Hours passed, and both Autobots and Decepticons found themselves in the _Nemesis_' infirmary; it was simply easier to tend to their wounds and discuss what should be done at the same time. The Doctor oversaw both repairs and talks, though only once or twice did he need to intervene in the latter. Jack and June, who had waited while Bulkhead and Bumblebee brought over Miko and Raf, briefly explained to the younger Humans what had happened.

"So Primus is really a bad guy?" Miko asked quietly, while the Cybertronians kept to their own council, "I would've thought he'd be like a Cybertronian Jesus or something."

"I wouldn't say he's evil," June said, "More like he's got a very skewed sense of right and wrong. Mostly that _his_ right is right, and organics are wrong."

"Sounds like a jerk," Miko commented.

"This will not stand!" Megatron roared, getting everyone's attention, "We should return to Cybertron and put an end to Primus' machinations _permanently_."

"Primus is the core of Cybertron!" Ratchet argued, "If we want our world to be restored, Primus cannot be harmed!"

"You both have a point," the Doctor said, "Primus can't be woken up again, he'd just exert more control over you, but is there a way to reactivate the core without that little side-effect?"

Optimus tapped his chin in thought, then turned to the Autobot medic. "Ratchet, what about the effects of Synthetic Energon? It was theorized that enough naturally-occurring Energon could reactivate the core, and with it, Primus, but what about artificially-made Energon?"

Ratchet opened his mouth, closed it again, then narrowed his optics in thought. He turned to Knockout, his Decepticon counterpart; both began talking so quickly that most of the others only caught snippets of the conversation.

After a moment, Ratchet turned to the others. "It's possible… we'd have to do a lot more tests, but in theory…"

Optimus held up a servo. "All we ask is that you try, old friend."

"Assuming we can restore Cybertron," Megatron said, crossing his arms, "We will need to establish a new government that doesn't rely on the teachings of Primus as the final say on matters."

"Agreed," Optimus said—the shock of agreeing with Megatron on _anything_ was still fresh, but he hid it well, "Perhaps a shared leadership between our two groups, and if we cannot agree on a matter between the two of us, an anonymous vote can be made by the populace?"

"That… could work," Megatron admitted, "We will have much to discuss on our way back to Cybertron."

The Doctor beamed. "See? Isn't it easier to just sit down and talk about these things?"

"It's certainly easier than finding out our own creator screwed us over," Bulkhead groused.

Early on in the discussions, it had been established that Primus would no longer be venerated, but demonized. No one had objected to that.

"While we finalize our truce," Optimus said, "Earth's governments must be informed that we will be leaving. We will have to remove any Cybertronian technology as well; that may take some time."

"We'll also need as much Energon as possible to sustain us until we get Cybertron's core up and running again," Ratchet added.

"That won't be a problem," Breakdown—a Decepticon who had accepted the sudden peace with a shrug—said, "We've identified most of the major Energon deposits on this planet; if we don't have to worry about fighting each other, we could devote more time to mining and get off this rock sooner."

"Probably a good idea," the Doctor said, "Energon and Humans—and most organics, now that I think about it—don't mix."

"Very well," Megatron said, standing up, "Let us make haste, so that we may depart from this misbegotten planet."

"Actually, Megatron," the Doctor said, "I need to speak to you and Optimus for a moment."

While the leaders stayed behind, the Autobots and Decepticons headed out to fulfill their duties; a nod from the Doctor had June guiding the children into the TARDIS, which would take them back to the Autobot base once the Doctor was done.

As soon as the three were alone, the Doctor leveled a hard stare at the Cybertronians. "I'm glad that you're reaching a peaceful resolution, I really am, but I have to warn you: if any Cybertronian goes to this or any other world with hostile intentions, I will know about it… and I will not be happy."

From his tone, both Optimus and Megatron figured that if the Doctor was unhappy, many Cybertronians would likely not live to see another day.

"We understand, Doctor," Optimus said, "We will enact laws to keep such things from happening."

The Doctor nodded. "Good. Glad to hear it."

The Time Lord began heading to the TARDIS, but this time, it was Optimus who stopped him.

"Doctor, do you know of the Matrix of Leadership?"

The Doctor thought about it for a moment, then shook his head, while Megatron looked at the Prime, intrigued.

"Within my chassis is an ancient relic from Primus, which passes down the knowledge and wisdom of the Primes before me, and indeed, the tenets of Primus himself."

"Don't sound so proud of that, Optimus," Megatron growled, but Optimus continued.

"Ever since you arrived, I have searched the Matrix for any knowledge about you. It was only recently that I discovered something concerning: a warning from Primus."

"About me?" the Doctor asked, "Considering how mad he was the last time we met, I wouldn't be surprised."

"It was not a warning _about _you," Optimus said, "but a warning _for _you. I am unsure of its meaning, however.

"When the fourth knock ends, so too shall the Doctor."

The Doctor went very still for a moment, and then gave both leaders his sternest stare. "Hurry up and get off Earth. I'd rather you not get caught in something that makes your own war look like an argument."

Without another word, the Doctor strode towards the TARDIS; a few moments later, the box slowly faded away.

…

**Jasper, Nevada**

It was with great reluctance that Miko and Raf exited the TARDIS and into the Autobots' base. They had completely freaked out when they'd seen the inside of the time machine, and had wanted to see more, but the Doctor had been firm when he'd said that they needed to be in the base.

"You know, we don't see you for years," Jack said, patting the outside of the TARDIS fondly, "and when you _do _show up again, you end a war that's lasted for millions of years, all in a day. Man, I missed this."

"Me too," June said, then smiled at the Doctor, "So, where are we going next?"

The Doctor suppressed a wince; this wasn't something he wanted to do.

"I'm sorry, June," he said sadly, "but this was the last time."

Both mother and son blinked.

"What? Why?" Jack asked.

"I travel alone now," the Doctor said, as solemn as they had ever seen him, "I can't risk the people I care about getting hurt, not anymore."

"But—" June began to protest, but the Doctor held up a hand to silence her.

"June, you and Jack have based your whole lives around me coming back," he said, "You're a brilliant nurse and could have a much better job just about anywhere in the world, but you've stayed here because you wanted to travel with me. You can't… you can't make me the focus of your world."

June flinched; the truth stung. "So… is this goodbye?"

The Doctor smiled. "You know I never say goodbye. Maybe we'll see each other again; after all, I've got all of time and space at my fingertips."

June and Jack seemed ready to argue, but both gave up; they knew there was little chance of changing the Doctor's mind once it was made up.

"When are you going to leave?" Jack asked.

The Doctor ruffled the boy's hair fondly. "I'd better leave soon. I have things I need to take care of."

June had tears in her eyes, but managed to keep herself from crying as she grabbed the Doctor by the shoulders.

"Even if we do see you again… I'd never forgive myself if I didn't do this."

Before the Doctor could ask what she was talking about, June wrapped her arms around his neck and kissed him. The kiss lasted for several seconds, and then June pulled away, blushing furiously, while Jack had his face buried in his hands, while the Doctor looked like someone had hit him over the head.

"Just… don't forget about us, okay?" June asked, looking at the Doctor shyly.

The Doctor smiled, much more tenderly this time. "I never will."

With that, the Last Time Lord walked into the TARDIS. As the wheezing, groaning sound began to echo around the base, Jack gave his mother a comforting one-armed hug. Despite the Doctor's words, as the TARDIS vanished, neither Darby was convinced that they would ever see the Time Lord again.

"What in the Sam Hill was that!?"

The Humans in the base turned to see a middle-aged, African American man in a slightly rumpled suit staring at where the TARDIS had been. He was Special Agent William Fowler, the U.S. liaison to the Autobots… and who had been completely left out of the loop about today's events.

Miko nonchalantly went back to looking over Raf's shoulder at whatever he was doing on his laptop.

"Eh, the usual: time-traveling aliens, boxes that are bigger on the inside… same old, same old."

Fowler spent a moment trying to process that, then gave up and groaned. "That's it, I'm taking a vacation."

Jack smirked, then looked back at his mother. "Are you going to be okay?"

"Are you?" June asked back.

Jack shrugged. "He was my friend, and I'll miss him, but… well, I didn't decide to kiss him, now did I?"

"I think I'll be okay," June said, "but I think he was right: it's time to move on with our lives.

"I know I have a few requests to go to other hospitals somewhere…"

**Yeah… I think I need to apologize for how long this chapter took. I'm sorry, I just got distracted by other stories and college and stuff.**

**So, some things to cover:**

**First, Primus as a bad guy (sort of): I never liked people who are 'the embodiment of order' and such stupid things. Who put you in charge!? Plus, since Primus was always a good guy in just about every story I've ever seen or read, I thought it was a neat twist.**

**The Autobot/Decepticon peace: I initially considered having the Doctor just destroy the Decepticons and then telling the Autobots to piss off and leave, but that didn't sit right with me. I like the idea of both sides getting really pissed at Primus for letting their entire society go to hell, and putting their differences aside just to spite him. Also, not every conflict has to end in an epic fight. Sometimes, you just need someone else to smack some sense into people.**

**The Master: This was a little thing I decided to throw in. I wanted a reason for Primus being a jackass, and I just saw the finale of the latest season of Doctor Who. I couldn't resist.**

**Now, this isn't the last chapter. I have a little epilogue planned, expect that up within the next couple of days. Also, this is the last chapter that I will ever write from this computer (a desktop) because I finally got a new laptop after my old one decided to die a couple months ago.**

**Where are we going?**

**Into muffins.**


	5. I Don't Want to Go

**DOCTOR WHO DOES NOT BELONG TO ME. TRANSFORMERS PRIME DOES NOT BELONG TO ME. THE RIGHT TO PUT THE TWO TOGETHER FOR NO MONEY WHATSOEVER, HOWEVER, BELONGS TO ME.**

**This chapter marks the end of my shortest legit story to date. Seriously, only five chapters? Ah, whatever; I had fun writing this, and I'm just happy to share it with the rest of you.**

Blue Box, Blue Bots

Epilogue

I Don't Want to Go

**The TARDIS**

The Doctor was dying. He knew it, expected it, and while he didn't welcome it, he certainly wasn't running from it. It had been the only way to save his friend, Wilbur; he owed the man that much after what had happened to Donna, and after he'd helped save the world from the Master and Rassilon. Without Wilbur, Gallifrey would have returned, and the Time War would have begun anew.

Even without all that, however, the Doctor would have still sacrificed himself to save Wilbur. That was just how he worked.

Still, that meant he was dying. Very soon, he would regenerate; he would still live, but not like he was now. With his regeneration at hand, the Doctor wanted to spend some time seeing those he loved one more time.

He'd seen most of them, but there were still a few left, and two of them were next on his list of stops. Clutching his side as a spike of pain ripped through him, he punched in the coordinates, pulled the lever, and the TARDIS took off.

…

**Jasper, Nevada**

"All right, thank you," June said into her phone, then smiled at what the person at the other end of the line said, "No, I'm actually already packed; I just need to have everything shipped to my new apartment… I look forward to working with you, too. Goodbye."

"Good news?" Jack asked, though he already knew the answer.

"They just wanted to know how soon I could get to work," June said, "Johns Hopkins is pretty busy."

June and Jack had had quite a year after the Doctor left. After the decision to finally move on with their lives, both Darbys had thrown themselves into improving their lot in life. Jack had learned quite a lot during his travels with the Doctor, and after applying himself, he was able to graduate high school a year early and earned a scholarship to Yale, along with free housing. According to some of the professors he'd met, the younger Darby could easily land a job with NASA if he wanted.

Then there was Jack's personal life; a few months ago, he'd gone on a date with Miko, mostly on a dare, and the two actually hit it off. With Jack going to college on the other side of the country, maintaining a relationship with the girl would be difficult, but Miko, not wanting to stay away from her beau, had begun applying herself in school, determined to join Jack at Yale. Raf was also shooting for that college, and with his brains, he was practically a guarantee. If Miko really put in the effort, all three of them would stay together.

June had been busy as well. As the Doctor said, she was a brilliant nurse, who had taken a job with fewer hours in order to take care of Jack. Now that her son was leaving to start his own life, she'd dug up a few old offers to go to more prestigious hospitals. In the end, she'd taken an offer from Johns Hopkins, who had been eager to acquire her skills. As bittersweet as having Jack out of the house would be, it would give June the opportunity to do what she loved: helping people. The fact that she'd be making more than twenty times her previous salary didn't hurt, either.

The older Darby wasn't the only adult Human moving up in the world; Agent Fowler was now Deputy Director of the CIA, and rumors were spreading about how he was already getting groomed to have 'Deputy' taken out of his title, though he still checked in with June and the kids from time to time.

If there was one thing that the Humans wish hadn't changed, however, was what happened to the Autobots. After leaving Earth, the Autobots had only been able to send the occasional report to their Human friends on what was happening, and it was unlikely that they would be able to visit, what with them being so busy.

After the truce was made, Ratchet, Knockout and the Decpticon scientist Shockwave put their collective helms together and found a way to restart Cybertron's core without waking up Primus. Using Synthetic Energon and primal Cyber-matter, they were able to get things working again. With a constant supply of Energon now available, Autobots and Decepticons alike across the universe came rushing back home. At the moment, differences were still being worked out—you don't get over eons of war in just one year—but things were starting to look up for all Cybertronians.

_All thanks to the Doctor, _June thought wistfully, even as she tried not to wince at the pain of the memory.

Jack seemed to read his mother's mind and wrapped an arm around her shoulders. "Hey, it'll be okay; he never says goodbye, and you know he'll always look out for us."

"Oh, really?" a low voice said from behind them, "I don't see anyone looking out for your sorry butt, Darby."

Both Jack and June turned to see a face that no one in Jasper liked seeing: Vince, the redheaded boy who had bullied Jack for years. That had changed a few months ago, when the jerk had been expelled for assaulting Miko; oddly enough, no one got on Jack's case when he beat his childhood tormentor senseless before handing him over to the police. Vince hadn't served time for his crime, likely due to his very influential family, but that same family had had enough of Vince's troublemaking; they'd cut all ties after keeping him out of prison, and if the dirt and grime coating Vince's clothes and skin were any indication, he'd been on the streets for a while.

Of course, none of that mattered right now, because Vince was leveling a pistol at them.

"You ruined my life, Darby," Vince snarled, "You took everything away from me! I might not get it all back, but I _will _get even! I'm going to kill you, your mommy, your girlfriend and that midget dork you hang out with!"

Jack felt an overwhelming urge to repeat his last encounter with Vince and break his face, but with a gun pointed at him, there wasn't much he could do—

Until a familiar humming noise filled the air, and Vince's pistol broke apart in his hand. The bully-turned-criminal only stared dumbly at the disassembled weapon, which gave Jack the perfect opportunity to drive a devastating left hook into Vince's face. Vince reeled back, hands going for his face, but Jack wasn't done, landing several more punches into his gut and throat, before finally _throwing _Vince over his shoulder to land painfully on the sidewalk. Jack took a moment to kick Vince in the head hard enough to knock him out before speaking.

"Threatening the people I love _and _attacking us in broad daylight?" Jack shook his head. "No wonder he was expelled, right, Mom?"

"Jack," June whispered, pointing across the street, "look."

Jack followed his mother's finger to see the Doctor putting away his sonic screwdriver and giving them a light smile. Both Darbys wanted to rush over to the Time Lord and say something, _anything_, but the sound of sirens caught their attention. Someone had seen what Vince was doing and called the police, and several patrol cars were almost there. By the time June and Jack looked back at where the Doctor had been, he was gone.

Jack gave June a hug. "See, Mom? I told you he'd look out for us."

June blinked back tears as she smiled. "You're right, Jack. Thank you, Doctor."

…

**London, January 1, 2005**

The Doctor smiled at the sight of the departing Rose Tyler, the first person to see the face he wore now; it seemed fitting that she would be the last to see it as well. Of course, he had had to go back in time to before he'd first met her, because the Rose Tyler who did know him was in another universe, where he would never see her again.

He sighed; he'd seen the people he needed to see, and now it was time. He began walking through the snow towards the TARDIS, when another spike of pain ripped through him. He fell to the ground, the snow cushioning his fall, but did nothing to alleviate the pain.

The Doctor gritted his teeth and started to pull himself up, but froze when he saw someone who should not have been on Earth at this point in time. It was a humanoid alien, with a bald head, slanted eyes and tentacles where the mouth would be. The creature wore a professional suit; in its hands was a white orb, attached to a white cord that disappeared within the tentacles.

It was an Ood, a race that had been lobotomized by greedy Humans and turned into slaves. The Doctor and his friend, Donna, had freed them. Most Ood looked the same, but the Doctor recognized this one: it was Ood Sigma, the unofficial spokesperson for the Ood.

Sigma's orb lit up as he suddenly spoke. "We will sing for you, Doctor; the universe will sing you to your sleep."

Sigma held his orb to his chest, and as the Doctor hauled himself upright, he could hear it: the beautiful, haunting melody of the Ood as they sang, their voices reaching across time and space. The rational part of the Doctor's mind knew that the song didn't actually give him the strength to make it to the TARDIS, but the rest of his mind told the rational part to shut up for a bit.

"This song is ending," Sigma said, as the Doctor opened the TARDIS's door, "but the story never ends."

The Doctor walked into the TARDIS and took off his coat; he hung it on one of the coral-like supports, then activated the engines. He didn't set a particular destination, and at the moment, he didn't care.

He looked at his hands, which had begun to glow with golden light; he thought back one last time to all the friends he'd had.

Rose, Jack Harkness, Martha, Donna, Jack and June Darby…

"I don't want to go," he said quietly, almost pleading.

It didn't stop the regeneration; an instant later, golden light poured from his body. The energies smashed the control room; machinery sparked, glass shattered, and fires kicked up, as the changes made themselves apparent.

The Doctor screamed in pain as he died… and was reborn. He was roughly the same height as before, but nowhere near as skinny; he was still slender, but not in a bad way. His brown hair was even longer than before, while his ears, nose, and especially his chin had changed.

Once the golden light faded, the Doctor looked down at his feet.

"Legs!" he cried, his voice now higher-pitched as he lifted one leg and kissed his knee. "I've still got legs! Good."

He then began inspecting his new body. "Arms, hands—ooh, fingers, lots of fingers! Ears, yes, eyes, okay, nose… eh, I've had worse. Chin… blimey! Hair," the Doctor raised a hand to his head and realized how long his hair was.

"I'm a girl!" the Doctor then realized he had an Adam's Apple, "No, no, I'm not a girl." He pulled his bangs down to get a good look at the color. "Argh, I'm still not ginger!"

The Doctor began looking around wildly. "There was something else, something _important_; I'm, I'm—"

An explosion nearby jogged his memory, as well as knocking him off-balance. As he grabbed a part of the controls to keep himself upright, the Doctor laughed.

"Oh, that's right, I'm crashing!" continuing to laugh, the Doctor ran around the controls, trying to keep the TARDIS stable as it plummeted down to Earth, at an unknown place and time.

The Doctor grinned; danger, excitement and a new adventure awaited him.

"Geronimo!"

**And that's that, folks! The Eleventh Doctor is here, on his way to see Amelia Pond and have all those adventures with her and Rory Williams. This story is officially over; for those of you who wanted to see the Eleventh meet Jack and June again, you're going to be disappointed, because that's very unlikely to happen. Sorry, no Amy and Rory meeting Jack and June, no awkward discoveries with June and the Doctor. This was meant to be a really short story, mostly for my own amusement. I hope you enjoyed it, and I hope you enjoy my other stories as well!**

**But you have no weapons, no muffins, no **_**plan**_**!**

**Yeah, and doesn't that scare you to death?**


End file.
